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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2016	Oct. 21, 2016
Document and Entity Information [Abstract]
Entity Registrant Name	VERTEX PHARMACEUTICALS INC / MA
Entity Central Index Key	0000875320
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Document Type	10-Q
Document Period End Date	Sep. 30, 2016
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q3
Amendment Flag	false
Entity Common Stock, Shares Outstanding (in shares)		248,033,389

Condensed Consolidated Statements of Operations (unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Revenues:
Product revenues, net	$ 409,689	$ 302,511	$ 1,229,750	$ 593,774
Royalty revenues	3,835	5,759	12,713	17,628
Collaborative revenues	259	1,546	1,008	2,999
Total revenues	413,783	309,816	1,243,471	614,401
Costs and expenses:
Cost of product revenues	53,222	30,269	147,165	55,059
Royalty expenses	855	1,691	2,813	6,068
Research and development expenses	272,370	246,284	799,238	685,741
Sales, general and administrative expenses	106,055	99,772	322,921	280,026
Restructuring expenses, net	8	1,826	1,038	682
Total costs and expenses	432,510	379,842	1,273,175	1,027,576
Loss from operations	(18,727)	(70,026)	(29,704)	(413,175)
Interest expense, net	(20,140)	(21,134)	(60,993)	(63,552)
Other (expenses) income, net	(167)	(1,326)	3,025	(5,025)
Loss before provision for income taxes	(39,034)	(92,486)	(87,672)	(481,752)
Provision for income taxes	503	1,330	24,118	31,760
Net loss	(39,537)	(93,816)	(111,790)	(513,512)
Loss (Income) attributable to noncontrolling interest	696	(1,333)	(33,207)	30,909
Net loss attributable to Vertex	$ (38,841)	$ (95,149)	$ (144,997)	$ (482,603)
Net loss:
Basic (usd per share)	$ (0.16)	$ (0.39)	$ (0.59)	$ (2.00)
Diluted (usd per share)	$ (0.16)	$ (0.39)	$ (0.59)	$ (2.00)
Shares used in per share calculations:
Basic (in shares)	244,920	241,969	244,529	240,749
Diluted (in shares)	244,920	241,969	244,529	240,749

Condensed Consolidated Statements of Comprehensive Loss (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Comprehensive Income (Loss), Net of Tax, Including Portion Attributable to Noncontrolling Interest [Abstract]
Net loss	$ (39,537)	$ (93,816)	$ (111,790)	$ (513,512)
Changes in other comprehensive loss:
Unrealized holding gains (losses) on marketable securities	(96)	56	104	186
Unrealized gains (losses) on foreign currency forward contracts, net of tax	2,149	4,546	1,936	572
Foreign currency translation adjustment	(2,508)	(1,384)	(7,709)	(164)
Total changes in other comprehensive loss	(455)	3,218	(5,669)	594
Comprehensive loss	(39,992)	(90,598)	(117,459)	(512,918)
Comprehensive (income) loss attributable to noncontrolling interest	696	(1,333)	(33,207)	30,909
Comprehensive loss attributable to Vertex	$ (39,296)	$ (91,931)	$ (150,666)	$ (482,009)

Condensed Consolidated Balance Sheets (unaudited) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 719,692	$ 714,768
Marketable securities, available for sale	408,749	327,694
Restricted cash and cash equivalents (VIE)	58,420	78,910
Accounts receivable, net	182,229	173,838
Inventories	71,799	57,207
Prepaid expenses and other current assets	61,012	54,736
Total current assets	1,501,901	1,407,153
Property and equipment, net	687,613	697,715
Intangible assets	284,340	284,340
Goodwill	50,384	50,384
Cost method investments	53,314	0
Notes receivable	0	30,000
Restricted cash	22,087	22,083
Other assets	10,002	6,912
Total assets	2,609,641	2,498,587
Current liabilities:
Accounts payable	50,914	74,942
Accrued expenses	292,015	305,820
Deferred revenues, current portion	9,247	16,296
Accrued restructuring expenses, current portion	3,923	7,894
Capital lease obligations, current portion	17,772	15,545
Senior secured term loan, current portion	297,751	71,296
Other liabilities, current portion	51,219	14,374
Total current liabilities	722,841	506,167
Deferred revenues, excluding current portion	6,559	9,714
Accrued restructuring expenses, excluding current portion	3,314	7,464
Capital lease obligations, excluding current portion	31,719	42,923
Deferred tax liability	133,270	110,439
Construction financing lease obligation, excluding current portion	473,073	472,611
Senior secured term loan, net of current portion and discount	0	223,863
Other liabilities, excluding current portion	30,524	31,778
Total liabilities	1,401,300	1,404,959
Commitments and contingencies
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at September 30, 2016 and December 31, 2015	0	0
Common stock, $0.01 par value; 500,000,000 and 500,000,000 shares authorized at September 30, 2016 and December 31, 2015, respectively; 248,028,962 and 246,306,818 shares issued and outstanding at September 30, 2016 and December 31, 2015, respectively	2,446	2,427
Additional paid-in capital	6,429,726	6,197,500
Accumulated other comprehensive (loss) income	(3,845)	1,824
Accumulated deficit	(5,406,781)	(5,261,784)
Total Vertex shareholders' equity	1,021,546	939,967
Noncontrolling interest	186,795	153,661
Total shareholders’ equity	1,208,341	1,093,628
Total liabilities and shareholders’ equity	$ 2,609,641	$ 2,498,587

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Preferred stock, par value (usd per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	1,000,000	1,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (usd per share)	$ 0.01	$ 0.01
Common stock, shares authorized	500,000,000	500,000,000
Common stock, shares issued	248,028,962	246,306,818
Common stock, shares outstanding	248,028,962	246,306,818

Condensed Consolidated Statements of Shareholders' Equity and Noncontrolling Interest (unaudited) - USD ($) shares in Thousands, $ in Thousands	Total	Total Vertex Shareholders’ Equity	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive (Loss) Income	Accumulated Deficit	Noncontrolling Interest
Balance (shares) at Dec. 31, 2014			241,764
Balance at Dec. 31, 2014	$ 1,096,183	$ 1,075,006	$ 2,385	$ 5,777,154	$ 917	$ (4,705,450)	$ 21,177
Increase (Decrease) in Stockholders' Equity
Other comprehensive loss, net of tax	594	594			594
Net loss	(513,512)	(482,603)				(482,603)	(30,909)
Issuance of common stock under benefit plans (shares)			3,882
Issuance of common stock under benefit plans	139,453	139,453	$ 34	139,419			0
Stock-based compensation expense	189,697	189,697		189,697			0
Noncontrolling interest upon consolidation	164,317						164,317
Balance (shares) at Sep. 30, 2015			245,646
Balance at Sep. 30, 2015	1,076,732	922,147	$ 2,419	6,106,270	1,511	(5,188,053)	154,585
Balance (shares) at Dec. 31, 2015			246,307
Balance at Dec. 31, 2015	1,093,628	939,967	$ 2,427	6,197,500	1,824	(5,261,784)	153,661
Increase (Decrease) in Stockholders' Equity
Other comprehensive loss, net of tax	(5,669)	(5,669)			(5,669)
Net loss	(111,790)	(144,997)				(144,997)	33,207
Issuance of common stock under benefit plans (shares)			1,722
Issuance of common stock under benefit plans	50,894	50,894	$ 19	50,875			0
Stock-based compensation expense	181,278	181,351		181,351			(73)
Balance (shares) at Sep. 30, 2016			248,029
Balance at Sep. 30, 2016	$ 1,208,341	$ 1,021,546	$ 2,446	$ 6,429,726	$ (3,845)	$ (5,406,781)	$ 186,795

Condensed Consolidated Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Cash flows from operating activities:
Net loss	$ (111,790)	$ (513,512)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Stock-based compensation expense	178,623	186,379
Depreciation and amortization expense	45,947	46,596
Deferred income taxes	23,544	7,793
Other non-cash items, net	(904)	(2,876)
Changes in operating assets and liabilities:
Accounts receivable, net	(9,760)	(88,735)
Inventories	(11,536)	(16,127)
Prepaid expenses and other assets	(8,979)	(23,737)
Accounts payable	(21,532)	6,283
Accrued expenses and other liabilities	26,121	45,163
Accrued restructuring expense	(8,151)	(28,051)
Deferred revenues	(10,204)	(13,751)
Net cash provided by (used in) operating activities	91,379	(394,575)
Cash flows from investing activities:
Purchases of marketable securities	(616,625)	(292,135)
Maturities of marketable securities	535,379	804,588
Expenditures for property and equipment	(41,775)	(32,775)
Decrease in restricted cash and cash equivalents (VIE)	20,490	14,830
Investments in other entities	(20,000)	0
Investment in CRISPR Series B preferred stock	(3,075)	0
(Increase) decrease in other assets	(90)	(982)
Increase in restricted cash and cash equivalents	(3)	(21,980)
Payment for acquisition of variable interest entity	0	(80,000)
Net cash (used in) provided by investing activities	(125,699)	391,546
Cash flows from financing activities:
Issuances of common stock under benefit plans	51,165	139,689
Payments on capital lease obligations	(13,330)	(16,515)
Payments on construction financing lease obligation	(356)	(281)
Proceeds from capital lease financing	2,030	13,386
Net cash provided by financing activities	39,509	136,279
Effect of changes in exchange rates on cash	(265)	(2,259)
Net increase in cash and cash equivalents	4,924	130,991
Cash and cash equivalents—beginning of period	714,768	625,259
Cash and cash equivalents—end of period	719,692	756,250
Supplemental disclosure of cash flow information:
Cash paid for interest	64,662	64,231
Cash received from (paid for) income taxes	1,617	(1,261)
Capitalization of costs related to construction financing lease obligation	824	0
Issuances of common stock exercises from employee benefit plans receivable	$ 19	$ (236)

Basis of Presentation and Accounting Policies	9 Months Ended
Basis of Presentation and Accounting Policies	Sep. 30, 2016
Accounting Policies [Abstract]
Basis of Presentation and Accounting Policies	Basis of Presentation and Accounting Policies Basis of Presentation The accompanying condensed consolidated financial statements are unaudited and have been prepared by Vertex Pharmaceuticals Incorporated ("Vertex" or the "Company") in accordance with accounting principles generally accepted in the United States of America ("GAAP"). The condensed consolidated financial statements reflect the operations of (i) the Company, (ii) its wholly-owned subsidiaries and (iii) consolidated variable interest entities (VIEs). All material intercompany balances and transactions have been eliminated. The Company operates in one segment, pharmaceuticals. Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the financial position and results of operations for the interim periods ended September 30, 2016 and 2015. The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year. These interim financial statements should be read in conjunction with the audited financial statements for the year ended December 31, 2015, which are contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 that was filed with the Securities and Exchange Commission (the “SEC”) on February 16, 2016 (the "2015 Annual Report on Form 10-K"). The Company has reclassified certain amounts in the condensed consolidated balance sheets for the period ended December 31, 2015 between Accounts receivables, net and Prepaid expenses and other current assets to conform to the current year presentation. Use of Estimates and Summary of Significant Accounting Policies The preparation of condensed consolidated financial statements in accordance with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates in these condensed consolidated financial statements have been made in connection with the calculation of revenues, inventories, research and development expenses, stock-based compensation expense, restructuring expense, the fair value of intangible assets, goodwill, contingent consideration, noncontrolling interest, the consolidation of VIEs, leases, the fair value of cash flow hedges and the provision for or benefit from income taxes. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances future projections that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known. The Company's significant accounting policies are described in Note A, "Nature of Business and Accounting Policies," in the 2015 Annual Report on Form 10-K. Recent Accounting Pronouncements In 2014, the Financial Accounting Standards Board (“FASB”) issued amended guidance applicable to revenue recognition that will be effective for the year ending December 31, 2018. Early adoption is permitted for the year-ending December 31, 2017. The new guidance applies a more principle based approach to recognizing revenue. The new guidance must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. In 2016, the FASB issued amended guidance applicable to leases that will be effective for the year ending December 31, 2019. Early adoption is permitted. This update requires an entity to recognize assets and liabilities for leases with lease terms of more than 12 months on the balance sheet. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. In 2016, the FASB issued amended guidance applicable to share-based compensation to employees that will be effective for the year ending December 31, 2017. Early adoption is permitted. This update simplifies the accounting for employee share-based payment transactions, including the accounting for income taxes, forfeitures, and statutory tax withholding requirements, as well as classification in the statement of cash flows. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. In 2016, the FASB issued amended guidance for the classification of certain cash receipts and cash payments on the statement of cash flows to reduce existing diversity in practice. The new accounting guidance is effective for the year ending December 31, 2017. Early adoption is permitted. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. For a discussion of other recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2015 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the nine months ended September 30, 2016 that had a material effect on its condensed consolidated financial statements.

Product Revenues, Net

9 Months Ended

Sep. 30, 2016

Product Revenues [Abstract]

Product Revenues, Net

The Company sells its products principally to a limited number of specialty pharmacy providers and selected regional wholesalers in North America as well as government-owned and supported customers in international markets (collectively, its “Customers”). The Company's Customers in North America subsequently resell the products to patients and health care providers. The Company recognizes net revenues from product sales upon delivery to the Customer as long as (i) there is persuasive evidence that an arrangement exists between the Company and the Customer, (ii) collectibility is reasonably assured and (iii) the price is fixed or determinable.

In order to conclude that the price is fixed or determinable, the Company must be able to (i) calculate its gross product revenues from sales to Customers and (ii) reasonably estimate its net product revenues upon delivery to its Customers' locations. The Company calculates gross product revenues based on the price that the Company charges its Customers. The Company estimates its net product revenues by deducting from its gross product revenues (a) trade allowances, such as invoice discounts for prompt payment and Customer fees, (b) estimated government and private payor rebates, chargebacks and discounts, (c) estimated reserves for expected product returns and (d) estimated costs of co-pay assistance programs for patients, as well as other incentives for certain indirect customers.

The Company makes significant estimates and judgments that materially affect the Company's recognition of net product revenues. In certain instances, the Company may be unable to reasonably conclude that the price is fixed or determinable at the time of delivery, in which case it defers the recognition of revenues. Once the Company is able to determine that the price is fixed or determinable, it recognizes the revenues associated with the units in which revenue recognition was deferred.

The following table summarizes activity in each of the product revenue allowance and reserve categories for the nine months ended September 30, 2016:



	Trade Allowances			Rebates, Chargebacks and Discounts			Product Returns			Other Incentives			Total
	(in thousands)
Balance at December 31, 2015	$	2,089		$	44,669		$	1,228		$	1,310		$	49,296
Provision related to current period sales	14,680			98,242			1,631			5,547			120,100
Adjustments related to prior period sales	(82		)	(1,081		)	(205		)	(80		)	(1,448		)
Credits/payments made	(14,505		)	(70,718		)	(345		)	(5,607		)	(91,175		)
Balance at September 30, 2016	$	2,182		$	71,112		$	2,309		$	1,170		$	76,773

In the three and nine months ended September 30, 2016, the Company sold ORKAMBI in France pursuant to early access programs. The Company has not recognized any product revenues based on these sales because the price is not fixed or determinable due to the ongoing negotiations regarding the reimbursement rate for ORKAMBI in France. If the negotiated reimbursement rate in France is lower than the price currently being paid by Customers in France under these programs, the Company would reimburse the difference between such prices to the Customers. The cash received from sales in France is included as a liability on the Company's condensed consolidated balance sheet, and the increase in "other liabilities, current portion" from December 31, 2015 to September 30, 2016 is primarily due to this liability.

Collaborative Arrangements

9 Months Ended

Sep. 30, 2016

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaborative Arrangements

Cystic Fibrosis Foundation Therapeutics Incorporated

The Company has a research, development and commercialization agreement with Cystic Fibrosis Foundation Therapeutics Incorporated (“CFFT”) that was originally entered into in May 2004, and was most recently amended on October 13, 2016 (the “2016 Amendment”). Pursuant to the agreement, as amended, the Company has agreed to pay royalties ranging from low single digits to mid-single digits on potential sales of certain compounds first synthesized and/or tested between March 1, 2014 and August 31, 2016 and tiered royalties ranging from single digits to sub-teens on any approved drugs first synthesized and/or tested during a research term on or before February 28, 2014, including KALYDECO (ivacaftor), ORKAMBI (lumacaftor in combination with ivacaftor), lumacaftor and VX-661 (tezacaftor). For combination products, such as ORKAMBI, sales will be allocated equally to each of the active pharmaceutical ingredients in the combination product consistent with the allocation of net sales for ORKAMBI since the Company began marketing ORKAMBI in mid-2015.

In each of the fourth quarter of 2015 and first quarter of 2016, CFFT earned a commercial milestone payment of $13.9 million from the Company upon achievement of certain sales levels of lumacaftor. There are no additional commercial milestone payments payable by the Company to CFFT pursuant to the agreement. Pursuant to the 2016 Amendment, the CFFT provided the Company an upfront program award of $75.0 million and agreed to provide development funding to the Company of up to $6.0 million annually.

The Company began marketing KALYDECO in the United States and certain countries in the European Union in 2012 and began marketing ORKAMBI in the United States in 2015. The Company received approval for ORKAMBI In the European Union in 2015 and in Canada and Australia in 2016. The Company has royalty obligations to CFFT for ivacaftor, lumacaftor and VX-661 until the expiration of patents covering those compounds. The Company has patents in the United States and European Union covering the composition-of-matter of ivacaftor that expire in 2027 and 2025, respectively, subject to potential patent extensions. The Company has patents in the United States and European Union covering the composition-of-matter of lumacaftor that expire in 2030 and 2026, respectively, subject to potential extension. The Company has patents in the United States and European Union covering the composition-of-matter of VX-661 (tezacaftor) that expire in 2027 and 2028, respectively, subject to potential extension.

CRISPR Therapeutics AG

In October 2015, the Company entered into a strategic collaboration, option and license agreement (the "CRISPR Agreement") with CRISPR Therapeutics AG and its affiliates ("CRISPR") to collaborate on the discovery and development of potential new treatments aimed at the underlying genetic causes of human diseases using CRISPR-Cas9 gene editing technology. The Company has the exclusive right to license up to six CRISPR-Cas9-based targets. In connection with the CRISPR Agreement, the Company made an upfront payment to CRISPR of $75.0 million and a $30.0 million investment in CRISPR pursuant to a convertible loan agreement that converted into preferred stock in January 2016. The Company expensed $75.0 million to research and development, and the $30.0 million investment was recorded at cost and is classified as a long-term asset on the Company’s condensed consolidated balance sheet. In the second quarter of 2016, the Company made an additional preferred stock investment in CRISPR of approximately $3.1 million. In connection with CRISPR's initial public offering in October 2016, the Company made an additional $10 million common share investment in CRISPR and the Company's preferred stock investment in CRISPR converted into common shares.

The Company will fund all of the discovery activities conducted pursuant to the CRISPR Agreement. For potential hemoglobinapathy treatments, including treatments for sickle cell disease, the Company and CRISPR will share equally all research and development costs and worldwide revenues. For other targets that the Company elects to license, the Company would lead all development and global commercialization activities. For each of up to six targets that the Company elects to license, other than hemoglobinapathy targets, CRISPR has the potential to receive up to $420.0 million in development, regulatory and commercial milestones and royalties on net product sales.

The Company may terminate the CRISPR Agreement upon 90 days’ notice to CRISPR prior to any product receiving marketing approval or upon 270 days’ notice after a product has received marketing approval. The CRISPR Agreement also may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, the CRISPR Agreement will continue in effect until the expiration of the Company's payment obligations under the CRISPR Agreement.

Variable Interest Entities

The Company has entered into several agreements pursuant to which it has licensed rights to certain drug candidates from third-party collaborators, which has resulted in the consolidation of the third parties' financial statements into the Company's condensed consolidated financial statements as VIEs. In order to account for the fair value of the contingent milestone and royalty payments related to these collaborations under GAAP, the Company uses present-value models based on assumptions regarding the probability of achieving the relevant milestones, estimates regarding the timing of achieving the milestones, estimates of future product sales and the appropriate discount rates. The Company bases its estimate of the probability of achieving the relevant milestones on industry data for similar assets and its own experience. The discount rates used in the valuation model represent a measure of credit risk and market risk associated with settling the liabilities. Significant judgment is used in determining the appropriateness of these assumptions at each reporting period. Changes in these assumptions could have a material effect on the fair value of the contingent milestone and royalty payments. The following collaborations are reflected in the Company's financial statements as consolidated VIEs:

Parion Sciences, Inc.

License and Collaboration Agreement

In June 2015, the Company entered into a strategic collaboration and license agreement (the "Parion Agreement") with Parion Sciences, Inc. (“Parion”). Pursuant to the Parion Agreement, the Company is collaborating with Parion to develop investigational epithelial sodium channel (“ENaC”) inhibitors, including VX-371 (formerly P-1037) and VX-551 (formerly P-1055), for the potential treatment of cystic fibrosis, or CF, and other pulmonary diseases. The Company is leading development activities for VX-371 and VX-551 and is responsible for all costs, subject to certain exceptions, related to development and commercialization of the compounds.

Pursuant to the Parion Agreement, the Company has worldwide development and commercial rights to Parion’s lead investigational ENaC inhibitors, VX-371 and VX-551, for the potential treatment of CF and all other pulmonary diseases and has the option to select additional compounds discovered in Parion’s research program. Parion received an $80.0 million up-front payment and has the potential to receive up to an additional (i) $490.0 million in development and regulatory milestone payments for development of ENaC inhibitors in CF, including $360.0 million related to global filing and approval milestones, (ii) $370.0 million in development and regulatory milestones for VX-371 and VX-551 in non-CF pulmonary indications and (iii) $230.0 million in development and regulatory milestones should the Company elect to develop an additional ENaC inhibitor from Parion’s research program. The Company has agreed to pay Parion tiered royalties that range from the low double digits to mid-teens as a percentage of potential sales of licensed products.

The Company may terminate the Parion Agreement upon 90 days’ notice to Parion prior to any licensed product receiving marketing approval or upon 180 days’ notice after a licensed product has received marketing approval. If the Company experiences a change of control prior to the initiation of the first Phase 3 clinical trial for a licensed product, Parion may terminate the Parion Agreement upon 30 days’ notice, subject to the Company's right to receive specified royalties on any subsequent commercialization of licensed products. The Parion Agreement also may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, the Parion Agreement will continue in effect until the expiration of the Company's royalty obligations, which expire on a country-by-country basis on the later of (i) the date the last-to-expire patent covering a licensed product expires or (ii) ten years after the first commercial sale in the country.

The Company determined that Parion is a VIE based on, among other factors, the significance to Parion of the ENaC inhibitors licensed to the Company pursuant to the Parion Agreement and on the Company's power to direct the activities that most significantly affect the economic performance of Parion. Accordingly, the Company consolidated Parion's financial statements beginning on June 4, 2015. However, the Company's interests in Parion are limited to those accorded to the Company in the Parion Agreement.

Consideration for the Parion Agreement

The Company determined that the fair value of the consideration from the Company to Parion was $255.3 million as of June 4, 2015, which consisted of (i) an $80.0 million up-front payment, (ii) the estimated fair value of the contingent research and development milestones potentially payable by the Company to Parion and (iii) the estimated fair value of potential royalty payments payable by the Company to Parion. The Company valued the contingent milestone and royalty payments using (a) discount rates ranging from 4.1% to 5.9% for the development milestones and (b) a discount rate of 6.6% for royalties. The consideration paid and the preliminary fair value of the contingent milestone and royalty payments payable by the Company pursuant to the agreement are set forth in the table below:



	June 4, 2015
	(in thousands)
Up-front payment	$	80,000
Fair value of contingent milestone and royalty payments	175,340
Total	$	255,340

Allocation of Assets and Liabilities

The Company allocated the total consideration to the assets and liabilities of Parion. The following table summarizes the final fair values of the assets and liabilities recorded on the effective date of the agreement:



	June 4, 2015
	(in thousands)
Intangible assets	$	255,340
Net assets attributable to noncontrolling interests	(164,317		)
Deferred tax liability	(91,023		)
Net other assets (liabilities)	(10,468		)
Goodwill	$	10,468

The Company recorded $255.3 million of intangible assets on the Company's condensed consolidated balance sheet for Parion's in-process research and development assets. These in-process research and development assets relate to Parion's pulmonary ENaC platform, including the intellectual property related to VX-371 and VX-551, that are licensed by Parion to the Company. The Company recorded Parion’s assets and liabilities including (i) the fair value of the intangible assets, (ii) the fair value of the net assets attributable to noncontrolling interest, and (iii) a deferred tax liability resulting from a basis difference in the intangible assets and certain other net liabilities held by Parion. The difference between the fair value of the consideration paid and the fair value of Parion’s net assets was recorded as goodwill.

BioAxone Biosciences, Inc.

In October 2014, the Company entered into a license and collaboration agreement (the “BioAxone Agreement”) with BioAxone Biosciences, Inc. (“BioAxone”), a privately-held biotechnology company, which resulted in the consolidation of BioAxone as a VIE beginning on October 1, 2014. The Company paid BioAxone initial payments of $10.0 million in the fourth quarter of 2014.

BioAxone has the potential to receive up to $90.0 million in milestones and fees, including development, regulatory and milestone payments and a license continuation fee. In addition, BioAxone would receive royalties and commercial milestones on future net product sales of VX-210, if any. The Company recorded an in-process research and development intangible asset of $29.0 million for VX-210 and a corresponding deferred tax liability of $11.3 million attributable to BioAxone. The Company holds an option to purchase BioAxone at a predetermined price. The option expires on the earliest of (a) the day the FDA accepts the Biologics License Application submission for VX-210, (b) the day the Company elects to continue the license instead of exercising the option to purchase BioAxone and (c) March 15, 2018, subject to the Company’s option to extend this date by one year.

Aggregate VIE Financial Information

An aggregate summary of net loss attributable to noncontrolling interest related to the Company's VIEs for the three and nine months ended September 30, 2016 and 2015 is as follows:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Loss attributable to noncontrolling interest before provision for income taxes	$	2,406		$	1,743		$	6,080		$	3,322
(Benefit from) provision for income taxes	(510		)	777			20,063			30,367
(Increase) decrease in fair value of contingent milestone and royalty payments	(1,200		)	(3,853		)	(59,350		)	(2,780		)
Net (income) loss attributable to noncontrolling interest	$	696		$	(1,333	)	$	(33,207	)	$	30,909

The increases in the fair value of the contingent milestone and royalty payments in the nine months ended September 30, 2016 were primarily due to a Phase 2 clinical trial of VX-371, a compound being developed pursuant to the Parion Agreement, achieving its primary safety endpoint in the second quarter of 2016. The fair value of the contingent milestone and royalty payments also reflects changes in market interest rates and the time value of money. During the three and nine months ended September 30, 2016 and 2015, the increase (decrease) in the fair value of the contingent milestone and royalty payments related to the Company's VIEs was as follows:



	Three Months Ended September 30,					Nine Months Ended September 30,
	2016		2015			2016		2015
	(in thousands)
Parion	$	1,100	$	4,481		$	58,500	$	2,860
BioAxone	100		(628		)	850		(80		)

As of September 30, 2016, the fair value of the contingent milestone and royalty payments related to the Parion Agreement and the BioAxone Agreement was $232.5 million and $28.8 million, respectively. As of December 31, 2015, the fair value of the contingent milestone and royalty payments related to the Parion collaboration and the BioAxone collaboration was $179.0 million and $28.0 million, respectively.

The following table summarizes items related to the Company's VIEs included in the Company's condensed consolidated balance sheets as of the dates set forth in the table:



	September 30, 2016		December 31, 2015
	(in thousands)
Restricted cash and cash equivalents (VIE)	$	58,420	$	78,910
Prepaid expenses and other current assets	2,360		3,138
Intangible assets	284,340		284,340
Goodwill	19,391		19,391
Other assets	382		455
Accounts payable	1,122		676
Taxes payable	6,263		24,554
Other current liabilities	1,121		7,100
Deferred tax liability, net	133,270		110,438
Other liabilities	300		300
Noncontrolling interest	186,795		153,661

The Company has recorded the VIEs' cash and cash equivalents as restricted cash and cash equivalents (VIE) because (i) the Company does not have any interest in or control over the VIEs' cash and cash equivalents and (ii) the Company's agreements with each VIE do not provide for the VIEs' cash and cash equivalents to be used for the development of the assets that the Company licensed from the applicable VIE. Assets recorded as a result of consolidating the Company's VIEs' financial condition into the Company's balance sheet do not represent additional assets that could be used to satisfy claims against the Company's general assets.

Other Collaborations

The Company has entered into various agreements pursuant to which it collaborates with third parties, including inlicensing and outlicensing arrangements. Although the Company does not consider any of these arrangements to be material, the most notable of these arrangements are described below.

Moderna Therapeutics, Inc.

In July 2016, the Company entered into a strategic collaboration and licensing agreement (the "Moderna Agreement") with Moderna Therapeutics, Inc. ("Moderna") pursuant to which the parties are seeking to identify and develop messenger Ribonucleic Acid ("mRNA") Therapeutics for the treatment of CF. In connection with the Moderna Agreement in the third quarter of 2016, the Company made an upfront payment to Moderna of $20.0 million and a $20.0 million cost-method investment in Moderna pursuant to a convertible promissory note that converted into preferred stock in August 2016. Moderna has the potential to receive future development and regulatory milestones of up to $275.0 million, including $220.0 million in approval and reimbursement milestones, as well as tiered royalty payments on future sales.

Under the terms of the Moderna Agreement, Moderna will lead discovery efforts and the Company will lead all preclinical, development and commercialization activities associated with the advancement of mRNA Therapeutics that result from this collaboration and will fund all expenses related to the collaboration.

The Company may terminate the Moderna Agreement by providing advanced notice to Moderna, with the required length of notice dependent on whether any product developed under the Moderna Agreement has received marketing approval. The Moderna Agreement also may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, the Moderna Agreement will continue in effect until the expiration of the Company's payment obligations under the Moderna Agreement.

Janssen Pharmaceuticals, Inc.

In June 2014, the Company entered into an agreement (the “Janssen Influenza Agreement”) with Janssen Pharmaceuticals, Inc. (“Janssen Inc.”), which was amended in October 2014 to clarify certain roles and responsibilities of the parties.

Pursuant to the Janssen Influenza Agreement, Janssen Inc. has an exclusive worldwide license to develop and commercialize certain drug candidates for the treatment of influenza, including VX-787. The Company received non-refundable payments of $35.0 million from Janssen Inc. in 2014, which were recorded as collaborative revenue. The Company has the potential to receive development, regulatory and commercial milestone payments as well as royalties on future product sales, if any. Janssen Inc. may terminate the Janssen Influenza Agreement, subject to certain exceptions, upon six months' notice.

Janssen Inc. is responsible for costs related to the development and commercialization of the compounds. During the three and nine months ended September 30, 2016, the Company recorded reimbursement for these development activities of $2.8 million and $10.6 million, respectively. During the three and nine months ended September 30, 2015, the Company recorded reimbursement for these development activities of $4.0 million and $18.7 million, respectively. The reimbursements are recorded as a reduction to development expense in the Company's condensed consolidated statements of operations primarily due to the fact that Janssen Inc. directs the activities and selects the suppliers associated with these activities.

Earnings Per Share

9 Months Ended

Sep. 30, 2016

Earnings Per Share [Abstract]

Earnings Per Share

Basic net loss per share attributable to Vertex common shareholders is based upon the weighted-average number of common shares outstanding during the period, excluding restricted stock and restricted stock units that have been issued but are not yet vested. Diluted net loss per share attributable to Vertex common shareholders is based upon the weighted-average number of common shares outstanding during the period plus additional weighted-average common equivalent shares outstanding during the period when the effect is dilutive.

The Company did not include the securities in the following table in the computation of the net loss per share attributable to Vertex common shareholders calculations because the effect would have been anti-dilutive during each period:



	Three Months Ended September 30,		Nine Months Ended September 30,
	2016	2015	2016	2015
	(in thousands)
Stock options	12,947	12,025	12,947	12,025
Unvested restricted stock and restricted stock units	3,624	3,367	3,624	3,367

Fair Value Measurements

9 Months Ended

Sep. 30, 2016

Fair Value Disclosures [Abstract]

Fair Value Measurements

The fair value of the Company’s financial assets and liabilities reflects the Company’s estimate of amounts that it would have received in connection with the sale of the assets or paid in connection with the transfer of the liabilities in an orderly transaction between market participants at the measurement date. In connection with measuring the fair value of its assets and liabilities, the Company seeks to maximize the use of observable inputs (market data obtained from sources independent from the Company) and to minimize the use of unobservable inputs (the Company’s assumptions about how market participants would price assets and liabilities). The following fair value hierarchy is used to classify assets and liabilities based on the observable inputs and unobservable inputs used in order to value the assets and liabilities:



Level 1:	Quoted prices in active markets for identical assets or liabilities. An active market for an asset or liability is a market in which transactions for the asset or liability occur with sufficient frequency and volume to provide pricing information on an ongoing basis.
Level 2:	Observable inputs other than Level 1 inputs. Examples of Level 2 inputs include quoted prices in active markets for similar assets or liabilities and quoted prices for identical assets or liabilities in markets that are not active.
Level 3:	Unobservable inputs based on the Company’s assessment of the assumptions that market participants would use in pricing the asset or liability.

The Company’s investment strategy is focused on capital preservation. The Company invests in instruments that meet the credit quality standards outlined in the Company’s investment policy. This policy also limits the amount of credit exposure to any one issue or type of instrument. As of September 30, 2016, the Company’s investments were primarily in money market funds, short-term government-sponsored enterprise securities, corporate debt securities and commercial paper.

As of September 30, 2016, all of the Company’s financial assets that were subject to fair value measurements were valued using observable inputs. The Company’s financial assets valued based on Level 1 inputs consisted of money market funds and short-term government-sponsored enterprise securities. The Company’s financial assets valued based on Level 2 inputs consisted of corporate debt securities and commercial paper, which consisted of investments in highly-rated investment-grade corporations.

The following table sets forth the Company’s financial assets (excluding VIE cash and cash equivalents) and liabilities subject to fair value measurements:



	Fair Value Measurements as of September 30, 2016
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial assets carried at fair value:
Cash equivalents:
Money market funds	$	101,844		$	101,844	$	—		$	—
Marketable securities:
Government-sponsored enterprise securities	130,431			130,431		—			—
Corporate debt securities	146,942			—		146,942			—
Commercial paper	131,376			—		131,376			—
Prepaid and other current assets:
Foreign currency forward contracts	7,644			—		7,644			—
Other assets:
Foreign currency forward contracts	217			—		217			—
Total financial assets	$	518,454		$	232,275	$	286,179		$	—
Financial liabilities carried at fair value:
Other liabilities, current portion:
Foreign currency forward contracts	$	(1,459	)	$	—	$	(1,459	)	$	—
Other liabilities, excluding current portion:
Foreign currency forward contracts	(315		)	—		(315		)	—
Total financial liabilities	$	(1,774	)	$	—	$	(1,774	)	$	—



	Fair Value Measurements as of December 31, 2015
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset position):
Cash equivalents:
Money market funds	$	199,507		$	199,507	$	—		$	—
Government-sponsored enterprise securities	85,994			85,994		—			—
Commercial paper	34,889			—		34,889			—
Corporate debt securities	11,533			—		11,533			—
Marketable securities:
Government-sponsored enterprise securities	87,162			87,162		—			—
Commercial paper	99,123			—		99,123			—
Corporate debt securities	141,409			—		141,409			—
Prepaid and other current assets:
Foreign currency forward contracts	5,161			—		5,161			—
Other assets:
Foreign currency forward contracts	605			$	—	605			$	—
Total financial assets	$	665,383		$	372,663	$	292,720		$	—
Financial instruments carried at fair value (liability position):
Other liabilities, current portion:
Foreign currency forward contracts	$	(769	)	$	—	$	(769	)	$	—
Other liabilities, excluding current portion:
Foreign currency forward contracts	(132		)	—		(132		)	—
Total financial liabilities	$	(901	)	$	—	$	(901	)	$	—

The Company's VIEs invested in cash equivalents consisting of money market funds of $57.9 million as of September 30, 2016, which are valued based on Level 1 inputs. These cash equivalents are not included in the table above. The Company’s noncontrolling interest related to VIEs includes the fair value of the contingent milestone and royalty payments, which are valued based on Level 3 inputs. Please refer to Note C, “Collaborative Arrangements,” for further information.

As of September 30, 2016, the fair value and carrying value of the Company's Term Loan was $297.8 million. The fair value of the Company's Term Loan was estimated based on Level 3 inputs computed using the effective interest rate of the Term Loan. The effective interest rate considers the timing and amount of estimated future interest payments as well as current market rates. Please refer to Note K, "Long-term Obligations" for further information regarding the Company's Term Loan.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Marketable Securities

9 Months Ended

Sep. 30, 2016

Cash and Cash Equivalents [Abstract]

Marketable Securities

A summary of the Company’s cash, cash equivalents and marketable securities is shown below:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
As of September 30, 2016
Cash and cash equivalents:
Cash and money market funds	$	719,692	$	—	$	—		$	719,692
Total cash and cash equivalents	$	719,692	$	—	$	—		$	719,692
Marketable securities:
Government-sponsored enterprise securities (due within 1 year)	130,404		29		(2		)	130,431
Commercial paper (due within 1 year)	131,099		277		—			131,376
Corporate debt securities (due within 1 year)	147,016		6		(80		)	146,942
Total marketable securities	$	408,519	$	312	$	(82	)	$	408,749
Total cash, cash equivalents and marketable securities	$	1,128,211	$	312	$	(82	)	$	1,128,441

As of December 31, 2015
Cash and cash equivalents:
Cash and money market funds	$	582,352	$	—	$	—		$	582,352
Government-sponsored enterprise securities	85,994		—		—			85,994
Commercial paper	34,889		—		—			34,889
Corporate debt securities	11,533		—		—			11,533
Total cash and cash equivalents	$	714,768	$	—	$	—		$	714,768
Marketable securities:
Government-sponsored enterprise securities (due within 1 year)	$	87,176	$	—	$	(14	)	$	87,162
Commercial paper (due within 1 year)	98,877		246		—			99,123
Corporate debt securities (due within 1 year)	141,515		—		(106		)	141,409
Total marketable securities	$	327,568	$	246	$	(120	)	$	327,694
Total cash, cash equivalents and marketable securities	$	1,042,336	$	246	$	(120	)	$	1,042,462

The Company has a limited number of marketable securities in insignificant loss positions as of September 30, 2016, which the Company does not intend to sell and has concluded it will not be required to sell before recovery of the amortized costs for the investment at maturity. There were no charges recorded for other-than-temporary declines in fair value of marketable securities nor gross realized gains or losses recognized in the three and nine months ended September 30, 2016 and 2015.

Accumulated Other Comprehensive (Loss) Income

9 Months Ended

Sep. 30, 2016

Equity [Abstract]

Accumulated Other Comprehensive (Loss) Income

A summary of the Company's changes in accumulated other comprehensive (loss) income by component is shown below:



	Foreign Currency Translation Adjustment			Unrealized Holding Gains on Marketable Securities		Unrealized Gains (Losses) on Foreign Currency Forward Contracts, net of tax			Total
	(in thousands)
Balance at December 31, 2015	$	(2,080	)	$	126	$	3,778		$	1,824
Other comprehensive (loss) income before reclassifications	(7,709		)	104		6,715			(890		)
Amounts reclassified from accumulated other comprehensive loss	—			—		(4,779		)	(4,779		)
Net current period other comprehensive (loss) income	$	(7,709	)	$	104	$	1,936		$	(5,669	)
Balance at September 30, 2016	$	(9,789	)	$	230	$	5,714		$	(3,845	)



	Foreign Currency Translation Adjustment			Unrealized Holding (Losses) Gains on Marketable Securities			Unrealized Gains (Losses) on Foreign Currency Forward Contracts			Total
	(in thousands)
Balance at December 31, 2014	$	(971	)	$	(123	)	$	2,011		$	917
Other comprehensive (loss) income before reclassifications	(164		)	186			4,072			4,094
Amounts reclassified from accumulated other comprehensive loss	—			—			(3,500		)	(3,500		)
Net current period other comprehensive (loss) income	$	(164	)	$	186		$	572		$	594
Balance at September 30, 2015	$	(1,135	)	$	63		$	2,583		$	1,511

- Definition

The entire disclosure for comprehensive income, which includes, but is not limited to, 1) the amount of income tax expense or benefit allocated to each component of other comprehensive income, including reclassification adjustments, 2) the reclassification adjustments for each classification of other comprehensive income and 3) the ending accumulated balances for each component of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 15
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e689-108580

Reference 2: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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-Subparagraph (SX 210.3-04)
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-Name Accounting Standards Codification
-Glossary Reclassification Adjustments
-URI http://asc.fasb.org/extlink&oid=6522872

+ Details

Hedging

9 Months Ended

Sep. 30, 2016

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Hedging

The Company maintains a hedging program intended to mitigate the effect of changes in foreign exchange rates for a portion of the Company’s forecasted product revenues denominated in certain foreign currencies. The program includes foreign currency forward contracts that are designated as cash flow hedges under GAAP having contractual durations from one to eighteen months.

The Company formally documents the relationship between foreign currency forward contracts (hedging instruments) and forecasted product revenues (hedged items), as well as the Company's risk management objective and strategy for undertaking various hedging activities, which includes matching all foreign currency forward contracts that are designated as cash flow hedges to forecasted transactions. The Company also formally assesses, both at the hedge’s inception and on an ongoing basis, whether the foreign currency forward contracts are highly effective in offsetting changes in cash flows of hedged items on a prospective and retrospective basis. If the Company determines that a (i) foreign currency forward contract is not highly effective as a cash flow hedge, (ii) foreign currency forward contract has ceased to be a highly effective hedge or (iii) forecasted transaction is no longer probable of occurring, the Company would discontinue hedge accounting treatment prospectively. The Company measures effectiveness based on the change in fair value of the forward contracts and the fair value of the hypothetical foreign currency forward contracts with terms that match the critical terms of the risk being hedged. As of September 30, 2016, all hedges were determined to be highly effective and the Company had not recorded any ineffectiveness related to the hedging program.

The following table summarizes the notional amount of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges:



	As of September 30, 2016		As of December 31, 2015
Foreign Currency	(in thousands)
Euro	$	156,245	$	103,362
British pound sterling	73,684		78,756
Australian dollar	26,550		27,167
Total foreign currency forward contracts	$	256,479	$	209,285

The following table summarizes the fair value of the Company's outstanding foreign currency forward contracts designated as cash flow hedges under GAAP included on the Company's condensed consolidated balance sheets:



As of September 30, 2016
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid and other current assets	$	7,644	Other liabilities, current portion	$	(1,459	)
Other assets	217		Other liabilities, excluding current portion	(315		)
Total assets	$	7,861	Total liabilities	$	(1,774	)



As of December 31, 2015
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid and other current assets	$	5,161	Other liabilities, current portion	$	(769	)
Other assets	605		Other liabilities, excluding current portion	(132		)
Total assets	$	5,766	Total liabilities	$	(901	)

The following table summarizes the potential effect of offsetting derivatives by type of financial instrument on the Company's condensed consolidated balance sheets:



	As of September 30, 2016
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	7,861		$	—	$	7,861		$	(1,774	)	$	6,087
Total liabilities	$	(1,774	)	$	—	$	(1,774	)	$	1,774		$	—



	As of December 31, 2015
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	5,766		$	—	$	5,766		$	(901	)	$	4,865
Total liabilities	$	(901	)	$	—	$	(901	)	$	901		$	—

- Definition

The entire disclosure for derivative instruments and hedging activities including, but not limited to, risk management strategies, non-hedging derivative instruments, assets, liabilities, revenue and expenses, and methodologies and assumptions used in determining the amounts.

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-Paragraph 4H
-URI http://asc.fasb.org/extlink&oid=64837297&loc=SL5624258-113959

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 30
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=35736893&loc=d3e80748-113994

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4K
-URI http://asc.fasb.org/extlink&oid=64837297&loc=SL5708775-113959

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4J
-URI http://asc.fasb.org/extlink&oid=64837297&loc=SL5708773-113959

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4A
-URI http://asc.fasb.org/extlink&oid=64837297&loc=SL5618551-113959

Reference 15: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 1B
-URI http://asc.fasb.org/extlink&oid=64837297&loc=SL5580258-113959

Reference 16: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4E
-URI http://asc.fasb.org/extlink&oid=64837297&loc=SL5624181-113959

Reference 17: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 25
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6886632&loc=d3e76258-113986

Reference 18: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=64837297&loc=d3e41638-113959

Reference 19: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(n))
-URI http://asc.fasb.org/extlink&oid=26873400&loc=d3e23780-122690

+ Details

Inventories

9 Months Ended

Sep. 30, 2016

Inventory Disclosure [Abstract]

Inventories

Inventories consisted of the following:



	As of September 30, 2016		As of December 31, 2015
	(in thousands)
Raw materials	$	9,824	$	8,696
Work-in-process	46,057		40,695
Finished goods	15,918		7,816
Total	$	71,799	$	57,207

Intangible Assets and Goodwill	9 Months Ended
Intangible Assets and Goodwill	Sep. 30, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible Assets and Goodwill	Intangible Assets and Goodwill Intangible Assets As of September 30, 2016 and December 31, 2015, in-process research and development intangible assets of $284.3 million were recorded on the Company's condensed consolidated balance sheet. In June 2015, in connection with entering into the Parion Agreement, the Company recorded an in-process research and development intangible asset of $255.3 million based on the Company’s estimate of the fair value of Parion’s lead investigational ENaC inhibitors, including VX-371 and VX-551, that were licensed by the Company from Parion. The Company aggregated the fair value of the ENaC inhibitors into a single intangible asset because the phase, nature and risks of development as well as the amount and timing of benefits associated with the assets were similar. In October 2014, the Company recorded an in-process research and development intangible asset of $29.0 million based on the Company’s estimate of the fair value of VX-210, a drug candidate for patients with spinal cord injuries that was licensed by the Company from BioAxone. The Company used discount rates of 7.1% and 7.5% in the present-value models to estimate the fair values of the ENaC inhibitors and VX-210 intangible assets, respectively. Goodwill As of September 30, 2016 and December 31, 2015, goodwill of $50.4 million was recorded on the Company's condensed consolidated balance sheet.

- Definition

The entire disclosure for the aggregate amount of goodwill and a description of intangible assets, which may include (a) for amortizable intangible assets (also referred to as finite-lived intangible assets), the carrying amount, the amount of any significant residual value, and the weighted-average amortization period, (b) for intangible assets not subject to amortization (also referred to as indefinite-lived intangible assets), the carrying amount, and (c) the amount of research and development assets acquired and written off in the period, including the line item in the income statement in which the amounts written off are aggregated, if not readily apparent from the income statement. Also discloses (a) for amortizable intangibles assets in total and by major class, the gross carrying amount and accumulated amortization, the total amortization expense for the period, and the estimated aggregate amortization expense for each of the five succeeding fiscal years, (b) for intangible assets not subject to amortization the carrying amount in total and by major class, and (c) for goodwill, in total and for each reportable segment, the changes in the carrying amount of goodwill during the period (including the aggregate amount of goodwill acquired, the aggregate amount of impairment losses recognized, and the amount of goodwill included in the gain (loss) on disposal of a reporting unit). If any part of goodwill has not been allocated to a reportable segment, discloses the unallocated amount and the reasons for not allocating. For each impairment loss recognized related to an intangible asset (excluding goodwill), discloses: (a) a description of the impaired intangible asset and the facts and circumstances leading to the impairment, (b) the amount of the impairment loss and the method for determining fair value, (c) the caption in the income statement or the statement of activities in which the impairment loss is aggregated, and (d) the segment in which the impaired intangible asset is reported. For each goodwill impairment loss recognized, discloses: (a) a description of the facts and circumstances leading to the impairment, (b) the amount of the impairment loss and the method of determining the fair value of the associated reporting unit, and (c) if a recognized impairment loss is an estimate not finalized and the reasons why the estimate is not final. May also disclose the nature and amount of any significant adjustments made to a previous estimate of an impairment loss.

+ References + Details

Long-term Obligations	9 Months Ended
Long-term Obligations	Sep. 30, 2016
Long-term Debt and Capital Lease Obligations [Abstract]
Long-term Obligations	Long-term Obligations Fan Pier Leases In 2011, the Company entered into two lease agreements, pursuant to which the Company leases approximately 1.1 million square feet of office and laboratory space in two buildings (the “Buildings”) at Fan Pier in Boston, Massachusetts (the “Fan Pier Leases”). The Company commenced lease payments in December 2013, and will make lease payments pursuant to the Fan Pier Leases through December 2028. The Company has an option to extend the term of the Fan Pier Leases for an additional ten years. Because the Company was involved in the construction project, the Company was deemed for accounting purposes to be the owner of the Buildings during the construction period and recorded project construction costs incurred by the landlord. Upon completion of the Buildings, the Company evaluated the Fan Pier Leases and determined that the Fan Pier Leases did not meet the criteria for “sale-leaseback” treatment. Accordingly, the Company began depreciating the asset and incurring interest expense related to the financing obligation in 2013. The Company bifurcates its lease payments pursuant to the Fan Pier Leases into (i) a portion that is allocated to the Buildings and (ii) a portion that is allocated to the land on which the Buildings were constructed. The portion of the lease obligations allocated to the land is treated as an operating lease that commenced in 2011. Property and equipment, net, included $492.3 million and $502.3 million as of September 30, 2016 and December 31, 2015, respectively, related to construction costs for the Buildings. The carrying value of the Company's lease agreement liability for the Buildings was $472.7 million and $473.0 million as of September 30, 2016 and December 31, 2015, respectively. San Diego Lease On December 2, 2015, the Company entered into a lease agreement for 3215 Merryfield Row, San Diego, California with ARE-SD Region No. 23, LLC. Pursuant to this agreement, the Company agreed to lease approximately 170,000 square feet of office and laboratory space in a building to be built in San Diego, California. The lease will commence upon completion of the building, scheduled for the first half of 2018, and will extend for 16 years from the commencement date. Pursuant to the lease agreement, during the initial 16-year term, the Company will pay an average of approximately $10.2 million per year in aggregate rent, exclusive of operating expenses. The Company has the option to extend the lease term for up to two additional five-year terms. Term Loan In July 2014, the Company entered into a credit agreement with the lenders party thereto, and Macquarie US Trading LLC ("Macquarie"), as administrative agent. The credit agreement provided for a $300.0 million senior secured term loan ("Macquarie Loan"). On October 13, 2016, the Company terminated and repaid all outstanding obligations under the Macquarie Loan. The Macquarie Loan initially bore interest at a rate of 7.2% per annum, which was reduced to 6.2% per annum based on the FDA's approval of ORKAMBI. The Term Loan bore interest at a rate of LIBOR plus 5.0% per annum during the third year of the term. If the Company had not terminated and repaid all outstanding obligations, the maturity date of all loans under the facilities was July 9, 2017. Based on the Company's evaluation of the Macquarie Loan, the Company determined that the Macquarie Loan contained several embedded derivatives. These embedded derivatives were clearly and closely related to the host instrument because they related to the Company's credit risk; therefore, they did not require bifurcation from the host instrument, the Macquarie Loan. The Company incurred $5.3 million in fees paid to Macquarie that were recorded as a discount on the Macquarie Loan and were recorded as interest expense using the effective interest method over the term of the loan in the Company’s condensed consolidated statements of operations. As of September 30, 2016 and December 31, 2015, the unamortized discount associated with the Macquarie Loan that was included in the senior secured term loan caption on the Company’s condensed consolidated balance sheet was $2.1 million and $4.6 million, respectively. Subsequent Event On October 13, 2016, the Company entered into a Credit Agreement (the “Credit Agreement”) with Bank of America, N.A., as administrative agent and the lenders referred to therein. The Credit Agreement provides for a $500.0 million revolving facility, $300.0 million of which was drawn at closing (the “Loans”). The Credit Agreement also provides that, subject to satisfaction of certain conditions, the Company may request that the borrowing capacity under the Credit Agreement be increased by an additional $300.0 million. The Credit Agreement matures on October 13, 2021. The proceeds of the borrowing under the Credit Agreement were used primarily to repay the Company's existing indebtedness under the Macquarie Loan. The Company will incur a charge of $2.2 million in the fourth quarter of 2016 related to a loss on extinguishment attributable to the Macquarie Loan. The Loans will bear interest, at the Company's option, at either a base rate or a Eurodollar rate, in each case plus an applicable margin. Under the Credit Agreement, the applicable margins on base rate loans range from 0.75% to 1.50% and the applicable margins on Eurodollar loans range from 1.75% to 2.5%, in each case based on the Company's consolidated leverage ratio (the ratio of the Company's total consolidated debt to the Company's trailing twelve-month EBITDA). The Loans are guaranteed by certain of the Company's domestic subsidiaries and secured by substantially all of the Company's assets and the assets of the Company's domestic subsidiaries (excluding intellectual property, owned and leased real property and certain other excluded property) and by the equity interests of the Company's subsidiaries, subject to certain exceptions. Under the terms of the Credit Agreement, the Company must maintain, subject to certain limited exceptions, a consolidated leverage ratio of 3.00 to 1.00 and consolidated EBITDA of at least $200.0 million, in each case to be measured on a quarterly basis. The Credit Agreement contains customary representations and warranties and usual and customary affirmative and negative covenants. The Credit Agreement also contains customary events of default. In the case of a continuing event of default, the administrative agent would be entitled to exercise various remedies, including the acceleration of amounts due under outstanding loans.

Stock-based Compensation Expense

9 Months Ended

Sep. 30, 2016

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Stock-based Compensation Expense

During the three and nine months ended September 30, 2016 and 2015, the Company recognized the following stock-based compensation expense:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Stock-based compensation expense by type of award:
Stock options	$	28,773		$	39,074		$	86,859		$	105,720
Restricted stock and restricted stock units	30,966			26,203			88,107			78,274
ESPP share issuances	2,425			1,738			6,385			5,703
Less stock-based compensation expense capitalized to inventories	(955		)	(1,281		)	(2,728		)	(3,318		)
Total stock-based compensation included in costs and expenses	$	61,209		$	65,734		$	178,623		$	186,379

Stock-based compensation expense by line item:
Research and development expenses	$	39,980		$	44,701		$	115,068		$	124,550
Sales, general and administrative expenses	21,229			21,033			63,555			61,829
Total stock-based compensation included in costs and expenses	$	61,209		$	65,734		$	178,623		$	186,379

The following table sets forth the Company's unrecognized stock-based compensation expense, net of estimated forfeitures, by type of award and the weighted-average period over which that expense is expected to be recognized:



	As of September 30, 2016
	Unrecognized Expense, Net of Estimated Forfeitures		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Stock options	$	185,148	2.66
Restricted stock and restricted stock units	$	206,336	2.57
ESPP share issuances	$	2,886	0.47

The following table summarizes information about stock options outstanding and exercisable at September 30, 2016:



	Options Outstanding				Options Exercisable
Range of Exercise Prices	Number Outstanding	Weighted-average Remaining Contractual Life	Weighted-average Exercise Price		Number Exercisable	Weighted-average Exercise Price
	(in thousands)	(in years)	(per share)		(in thousands)	(per share)
$18.93–$20.00	137	1.35	$	18.93	137	$	18.93
$20.01–$40.00	1,816	3.32	$	34.08	1,815	$	34.07
$40.01–$60.00	1,937	5.89	$	48.19	1,719	$	48.57
$60.01–$80.00	1,348	7.38	$	75.90	809	$	75.51
$80.01–$100.00	4,598	8.74	$	90.62	1,271	$	89.38
$100.01–$120.00	1,627	8.33	$	109.33	606	$	109.29
$120.01–$134.69	1,484	8.80	$	130.60	510	$	130.06
Total	12,947	7.29	$	80.99	6,867	$	66.29

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References + Details

Other Arrangements	9 Months Ended
Other Arrangements	Sep. 30, 2016
Other Income and Expenses [Abstract]
Other Arrangements	Other Arrangements Sale of HIV Protease Inhibitor Royalty Stream In 2008, the Company sold to a third party its rights to receive royalty payments from GlaxoSmithKline plc, net of royalty amounts to be earned by and due to a third party, for a one-time cash payment of $160.0 million. These royalty payments relate to net sales of HIV protease inhibitors, which had been developed pursuant to a collaboration agreement between the Company and GlaxoSmithKline plc. As of September 30, 2016, the Company had $15.8 million in deferred revenues related to the one-time cash payment, which it is recognizing over the life of the collaboration agreement with GlaxoSmithKline plc based on the units-of-revenue method. In addition, the Company continues to recognize royalty revenues equal to the amount of the third-party subroyalty and an offsetting royalty expense for the third-party subroyalty payment.

Income Taxes	9 Months Ended
Income Taxes	Sep. 30, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company is subject to United States federal, state, and foreign income taxes. For the three and nine months ended September 30, 2016, the Company recorded a provision for income taxes of $0.5 million and $24.1 million, respectively. The provision for income taxes recorded in the three and nine months ended September 30, 2016 included a benefit of $0.5 million and a provision of $20.1 million, respectively, related to the Company's VIEs' income tax provision. The Company has no liability for taxes payable by the Company's VIEs and the income tax provision and related liability have been allocated to noncontrolling interest (VIE). For the three and nine months ended September 30, 2015, the Company recorded a provision for income taxes of $1.3 million and $31.8 million, respectively, primarily related to the Company's VIEs' income tax provision. As of September 30, 2016 and December 31, 2015, the Company had unrecognized tax benefits of zero and $0.4 million, respectively. The Company recognizes interest and penalties related to income taxes as a component of income tax expense. As of September 30, 2016, no interest and penalties have been accrued. The Company does not expect that its unrecognized tax benefits will materially increase within the next twelve months. The Company did not recognize any material interest or penalties related to uncertain tax positions as of September 30, 2016 and December 31, 2015. For the three months ended September 30, 2016, the Company reduced the balance of its unrecognized tax benefits by approximately $0.4 million due to the expiration of statute of limitations, which reduced the Company’s effective tax rate. The Company continues to maintain a valuation allowance against certain deferred tax assets where it is more likely than not that the deferred tax asset will not be realized because of its extended history of annual losses. The Company files United States federal income tax returns and income tax returns in various state, local and foreign jurisdictions. The Company is no longer subject to any tax assessment from an income tax examination in the United States before 2011 or any other major taxing jurisdiction for years before 2009, except where the Company has net operating losses or tax credit carryforwards that originated before 2009. The Company currently is under examination by the Internal Revenue Service for the year ended December 31, 2011 and in Delaware, Canada and Quebec for varying periods including the years ended December 31, 2011 through 2014. No adjustments have been reported. The Company is not under examination by any other jurisdictions for any tax year. The Company concluded audits with Pennsylvania and Texas during 2016 and Massachusetts and New York during 2015 with no material adjustments. The Company currently intends to reinvest the total amount of its unremitted earnings. At September 30, 2016, foreign earnings, which were not significant, have been retained indefinitely by foreign subsidiary companies for reinvestment; therefore, no provision has been made for income taxes that would be payable upon the distribution of such earnings, and it would not be practicable to determine the amount of the related unrecognized deferred income tax liability. Upon repatriation of those earnings, in the form of dividends or otherwise, the Company would be subject to United States federal income taxes (subject to an adjustment for foreign tax credits) and withholding taxes payable to the various foreign countries.

Restructuring Liabilities

9 Months Ended

Sep. 30, 2016

Restructuring and Related Activities [Abstract]

Restructuring Liabilities

2003 Kendall Restructuring

In 2003, the Company adopted a plan to restructure its operations to coincide with its increasing internal emphasis on advancing drug candidates through clinical development to commercialization. The restructuring liability relates to specialized laboratory and office space that is leased to the Company pursuant to a 15-year lease that terminates in 2018. The Company has not used more than 50% of this space since it adopted the plan to restructure its operations in 2003. This unused laboratory and office space currently is subleased to third parties.

The activities related to the restructuring liability for the three and nine months ended September 30, 2016 and 2015 were as follows:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Liability, beginning of the period	$	6,388		$	9,924		$	7,944		$	11,596
Cash payments	(5,340		)	(3,975		)	(13,104		)	(10,544		)
Cash received from subleases	2,866			2,919			8,882			8,194
Restructuring expense (income)	30			146			222			(232		)
Liability, end of the period	$	3,944		$	9,014		$	3,944		$	9,014

Fan Pier Move Restructuring

In connection with the relocation of its Massachusetts operations to Fan Pier in Boston, Massachusetts, which commenced in 2013, the Company is incurring restructuring charges related to its remaining lease obligations at its facilities in Cambridge, Massachusetts. The majority of these restructuring charges were recorded in the third quarter of 2014 upon decommissioning three facilities in Cambridge. During the first quarter of 2015, the Company terminated two of these lease agreements resulting in a credit to restructuring expense equal to the difference between the Company’s estimated future cash flows related to its lease obligations for these facilities and the termination payment paid to the Company’s landlord on the effective date of the termination. The third major facility included in this restructuring activity is 120,000 square feet of the Kendall Square Facility that the Company continued to use for its operations following its 2003 Kendall Restructuring. The rentable square footage in this portion of the Kendall Square Facility was subleased to a third party in February 2015. The Company will continue to incur charges through April 2018 related to the difference between the Company’s estimated future cash flows related to this portion of the Kendall Square Facility, which include an estimate for sublease income to be received from the Company's sublessee and its actual cash flows. The Company discounted the estimated cash flows related to this restructuring activity at a discount rate of 9%.

The activities related to the restructuring liability for the three and nine months ended September 30, 2016 and 2015 were as follows:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Liability, beginning of the period	$	4,863		$	9,017		$	5,964		$	33,390
Cash payments	(4,199		)	(3,070		)	(10,451		)	(25,421		)
Cash received from subleases	2,539			1,820			7,308			1,820
Restructuring expense (income)	90			51			472			(1,971		)
Liability, end of the period	$	3,293		$	7,818		$	3,293		$	7,818

Other Restructuring Activities

The Company has engaged in several other restructuring activities that are unrelated to its 2003 Kendall Restructuring and the Fan Pier Move Restructuring. The most significant activity commenced in October 2013 when the Company adopted a restructuring plan that included (i) a workforce reduction primarily related to the commercial support of INCIVEK following the continued and rapid decline in the number of patients being treated with INCIVEK as new medicines for the treatment of HCV infection neared approval and (ii) the write-off of certain assets. This action resulted from the Company's decision to focus its investment on future opportunities in CF and other research and development programs.

The activities related to the Company's other restructuring liabilities for the three and nine months ended September 30, 2016 and 2015 were as follows:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Liability, beginning of the period	$	1,233		$	902		$	1,450		$	869
Cash payments	(1,121		)	(1,559		)	(1,794		)	(2,782		)
Restructuring expense	(112		)	1,629			344			2,885
Liability, end of the period	$	—		$	972		$	—		$	972

Commitments and Contingencies	9 Months Ended
Commitments and Contingencies	Sep. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Financing Arrangements As of September 30, 2016, the Company had irrevocable stand-by letters of credit outstanding that were issued in connection with property leases and other similar agreements totaling $21.9 million that were cash collateralized. The cash used to support these letters of credit is included in restricted cash, as of September 30, 2016, on the Company's condensed consolidated balance sheet. Effective as of October 13, 2016, the letters of credit are covered by the Company's credit agreement with Bank of America, N.A., as administrative agent and the lenders referred to therein, and as a result, are no longer cash collateralized. Litigation On May 28, 2014, a purported shareholder class action Local No. 8 IBEW Retirement Plan & Trust v. Vertex Pharmaceuticals Incorporated, et al. was filed in the United States District Court for the District of Massachusetts, naming the Company and certain of the Company's current and former officers and directors as defendants. The lawsuit alleged that the Company made material misrepresentations and/or omissions of material fact in the Company's disclosures during the period from May 7, 2012 through May 29, 2012, all in violation of Section 10(b) of the Securities Exchange Act of 1934, as amended, and Rule 10b-5 promulgated thereunder. The purported class consists of all persons (excluding defendants) who purchased the Company’s common stock between May 7, 2012 and May 29, 2012. The plaintiffs seek unspecified monetary damages, costs and attorneys’ fees as well as disgorgement of the proceeds from certain individual defendants’ sales of the Company’s stock. On October 8, 2014, the Court approved Local No. 8 IBEW Retirement Fund as lead plaintiff, and Scott and Scott LLP as lead counsel for the plaintiff and the putative class. On February 23, 2015, the Company filed a reply to the plaintiffs’ opposition to its motion to dismiss. The court heard oral argument on the motion to dismiss on March 6, 2015 and took the motion under advisement. On September 30, 2015, the court granted the Company's motion to dismiss. On October 15, 2015, the plaintiff filed a notice of appeal. The First Circuit Court of Appeals issued a scheduling order on December 24, 2015. On February 2, 2016, the Plaintiff filed their opening brief and the Company filed its opposition brief on March 7, 2016. On March 24, 2016, the plaintiff filed their reply brief. Oral argument on the appeal took place on July 26, 2016. On October 3, 2016, the First Circuit Court of Appeals affirmed the district court’s dismissal of the Plaintiff’s complaint. As of September 30, 2016, the Company has not recorded any reserves for this purported class action. Guaranties and Indemnifications As permitted under Massachusetts law, the Company’s Articles of Organization and By-laws provide that the Company will indemnify certain of its officers and directors for certain claims asserted against them in connection with their service as an officer or director. The maximum potential amount of future payments that the Company could be required to make under these indemnification provisions is unlimited. However, the Company has purchased directors’ and officers’ liability insurance policies that could reduce its monetary exposure and enable it to recover a portion of any future amounts paid. No indemnification claims currently are outstanding, and the Company believes the estimated fair value of these indemnification arrangements is minimal. The Company customarily agrees in the ordinary course of its business to indemnification provisions in agreements with clinical trial investigators and sites in its drug development programs, sponsored research agreements with academic and not-for-profit institutions, various comparable agreements involving parties performing services for the Company and its real estate leases. The Company also customarily agrees to certain indemnification provisions in its drug discovery, development and commercialization collaboration agreements. With respect to the Company’s clinical trials and sponsored research agreements, these indemnification provisions typically apply to any claim asserted against the investigator or the investigator’s institution relating to personal injury or property damage, violations of law or certain breaches of the Company’s contractual obligations arising out of the research or clinical testing of the Company’s compounds or drug candidates. With respect to lease agreements, the indemnification provisions typically apply to claims asserted against the landlord relating to personal injury or property damage caused by the Company, to violations of law by the Company or to certain breaches of the Company’s contractual obligations. The indemnification provisions appearing in the Company’s collaboration agreements are similar to those for the other agreements discussed above, but in addition provide some limited indemnification for its collaborator in the event of third-party claims alleging infringement of intellectual property rights. In each of the cases above, the indemnification obligation generally survives the termination of the agreement for some extended period, although the Company believes the obligation typically has the most relevance during the contract term and for a short period of time thereafter. The maximum potential amount of future payments that the Company could be required to make under these provisions is generally unlimited. The Company has purchased insurance policies covering personal injury, property damage and general liability that reduce its exposure for indemnification and would enable it in many cases to recover all or a portion of any future amounts paid. The Company has never paid any material amounts to defend lawsuits or settle claims related to these indemnification provisions. Accordingly, the Company believes the estimated fair value of these indemnification arrangements is minimal. Other Contingencies The Company has certain contingent liabilities that arise in the ordinary course of its business activities. The Company accrues a reserve for contingent liabilities when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. There were no material contingent liabilities accrued as of September 30, 2016 or December 31, 2015.

Basis of Presentation and Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2016
Accounting Policies [Abstract]
Basis of Presentation	Basis of Presentation The accompanying condensed consolidated financial statements are unaudited and have been prepared by Vertex Pharmaceuticals Incorporated ("Vertex" or the "Company") in accordance with accounting principles generally accepted in the United States of America ("GAAP"). The condensed consolidated financial statements reflect the operations of (i) the Company, (ii) its wholly-owned subsidiaries and (iii) consolidated variable interest entities (VIEs). All material intercompany balances and transactions have been eliminated. The Company operates in one segment, pharmaceuticals. Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the financial position and results of operations for the interim periods ended September 30, 2016 and 2015. The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year. These interim financial statements should be read in conjunction with the audited financial statements for the year ended December 31, 2015, which are contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 that was filed with the Securities and Exchange Commission (the “SEC”) on February 16, 2016 (the "2015 Annual Report on Form 10-K"). The Company has reclassified certain amounts in the condensed consolidated balance sheets for the period ended December 31, 2015 between Accounts receivables, net and Prepaid expenses and other current assets to conform to the current year presentation.
Use of Estimates and Summary of Significant Accounting Policies	Use of Estimates and Summary of Significant Accounting Policies The preparation of condensed consolidated financial statements in accordance with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates in these condensed consolidated financial statements have been made in connection with the calculation of revenues, inventories, research and development expenses, stock-based compensation expense, restructuring expense, the fair value of intangible assets, goodwill, contingent consideration, noncontrolling interest, the consolidation of VIEs, leases, the fair value of cash flow hedges and the provision for or benefit from income taxes. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances future projections that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.
Recent Accounting Pronouncements	Recent Accounting Pronouncements In 2014, the Financial Accounting Standards Board (“FASB”) issued amended guidance applicable to revenue recognition that will be effective for the year ending December 31, 2018. Early adoption is permitted for the year-ending December 31, 2017. The new guidance applies a more principle based approach to recognizing revenue. The new guidance must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. In 2016, the FASB issued amended guidance applicable to leases that will be effective for the year ending December 31, 2019. Early adoption is permitted. This update requires an entity to recognize assets and liabilities for leases with lease terms of more than 12 months on the balance sheet. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. In 2016, the FASB issued amended guidance applicable to share-based compensation to employees that will be effective for the year ending December 31, 2017. Early adoption is permitted. This update simplifies the accounting for employee share-based payment transactions, including the accounting for income taxes, forfeitures, and statutory tax withholding requirements, as well as classification in the statement of cash flows. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. In 2016, the FASB issued amended guidance for the classification of certain cash receipts and cash payments on the statement of cash flows to reduce existing diversity in practice. The new accounting guidance is effective for the year ending December 31, 2017. Early adoption is permitted. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. For a discussion of other recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2015 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the nine months ended September 30, 2016 that had a material effect on its condensed consolidated financial statements.

Product Revenues, Net (Tables)

9 Months Ended

Sep. 30, 2016

Product Revenues [Abstract]

Schedule of product revenue allowances and reserve categories

The following table summarizes activity in each of the product revenue allowance and reserve categories for the nine months ended September 30, 2016:



	Trade Allowances			Rebates, Chargebacks and Discounts			Product Returns			Other Incentives			Total
	(in thousands)
Balance at December 31, 2015	$	2,089		$	44,669		$	1,228		$	1,310		$	49,296
Provision related to current period sales	14,680			98,242			1,631			5,547			120,100
Adjustments related to prior period sales	(82		)	(1,081		)	(205		)	(80		)	(1,448		)
Credits/payments made	(14,505		)	(70,718		)	(345		)	(5,607		)	(91,175		)
Balance at September 30, 2016	$	2,182		$	71,112		$	2,309		$	1,170		$	76,773

Collaborative Arrangements (Tables)

9 Months Ended

Sep. 30, 2016

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Fair Value Of Consideration Transferred

The consideration paid and the preliminary fair value of the contingent milestone and royalty payments payable by the Company pursuant to the agreement are set forth in the table below:



	June 4, 2015
	(in thousands)
Up-front payment	$	80,000
Fair value of contingent milestone and royalty payments	175,340
Total	$	255,340

Schedule of Collaborative Arrangement Activity Net Loss Attributable to Noncontrolling Interest

An aggregate summary of net loss attributable to noncontrolling interest related to the Company's VIEs for the three and nine months ended September 30, 2016 and 2015 is as follows:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Loss attributable to noncontrolling interest before provision for income taxes	$	2,406		$	1,743		$	6,080		$	3,322
(Benefit from) provision for income taxes	(510		)	777			20,063			30,367
(Increase) decrease in fair value of contingent milestone and royalty payments	(1,200		)	(3,853		)	(59,350		)	(2,780		)
Net (income) loss attributable to noncontrolling interest	$	696		$	(1,333	)	$	(33,207	)	$	30,909

Changes In Fair Value Of Contingent Consideration

During the three and nine months ended September 30, 2016 and 2015, the increase (decrease) in the fair value of the contingent milestone and royalty payments related to the Company's VIEs was as follows:



	Three Months Ended September 30,					Nine Months Ended September 30,
	2016		2015			2016		2015
	(in thousands)
Parion	$	1,100	$	4,481		$	58,500	$	2,860
BioAxone	100		(628		)	850		(80		)

Schedule Of Collaborative Arrangement Summary Of Items Related To Variable Interest Entities

The following table summarizes items related to the Company's VIEs included in the Company's condensed consolidated balance sheets as of the dates set forth in the table:



	September 30, 2016		December 31, 2015
	(in thousands)
Restricted cash and cash equivalents (VIE)	$	58,420	$	78,910
Prepaid expenses and other current assets	2,360		3,138
Intangible assets	284,340		284,340
Goodwill	19,391		19,391
Other assets	382		455
Accounts payable	1,122		676
Taxes payable	6,263		24,554
Other current liabilities	1,121		7,100
Deferred tax liability, net	133,270		110,438
Other liabilities	300		300
Noncontrolling interest	186,795		153,661

Schedule of Recognized Identified Assets Acquired and Liabilities Assumed

The following table summarizes the final fair values of the assets and liabilities recorded on the effective date of the agreement:



	June 4, 2015
	(in thousands)
Intangible assets	$	255,340
Net assets attributable to noncontrolling interests	(164,317		)
Deferred tax liability	(91,023		)
Net other assets (liabilities)	(10,468		)
Goodwill	$	10,468

Earnings Per Share (Tables)

9 Months Ended

Sep. 30, 2016

Earnings Per Share [Abstract]

Potential gross common equivalent shares



	Three Months Ended September 30,		Nine Months Ended September 30,
	2016	2015	2016	2015
	(in thousands)
Stock options	12,947	12,025	12,947	12,025
Unvested restricted stock and restricted stock units	3,624	3,367	3,624	3,367

Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2016

Fair Value Disclosures [Abstract]

Financial assets subject to fair value measurements (excluding restricted cash and cash equivalents (Alios))

The following table sets forth the Company’s financial assets (excluding VIE cash and cash equivalents) and liabilities subject to fair value measurements:



	Fair Value Measurements as of September 30, 2016
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial assets carried at fair value:
Cash equivalents:
Money market funds	$	101,844		$	101,844	$	—		$	—
Marketable securities:
Government-sponsored enterprise securities	130,431			130,431		—			—
Corporate debt securities	146,942			—		146,942			—
Commercial paper	131,376			—		131,376			—
Prepaid and other current assets:
Foreign currency forward contracts	7,644			—		7,644			—
Other assets:
Foreign currency forward contracts	217			—		217			—
Total financial assets	$	518,454		$	232,275	$	286,179		$	—
Financial liabilities carried at fair value:
Other liabilities, current portion:
Foreign currency forward contracts	$	(1,459	)	$	—	$	(1,459	)	$	—
Other liabilities, excluding current portion:
Foreign currency forward contracts	(315		)	—		(315		)	—
Total financial liabilities	$	(1,774	)	$	—	$	(1,774	)	$	—



	Fair Value Measurements as of December 31, 2015
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset position):
Cash equivalents:
Money market funds	$	199,507		$	199,507	$	—		$	—
Government-sponsored enterprise securities	85,994			85,994		—			—
Commercial paper	34,889			—		34,889			—
Corporate debt securities	11,533			—		11,533			—
Marketable securities:
Government-sponsored enterprise securities	87,162			87,162		—			—
Commercial paper	99,123			—		99,123			—
Corporate debt securities	141,409			—		141,409			—
Prepaid and other current assets:
Foreign currency forward contracts	5,161			—		5,161			—
Other assets:
Foreign currency forward contracts	605			$	—	605			$	—
Total financial assets	$	665,383		$	372,663	$	292,720		$	—
Financial instruments carried at fair value (liability position):
Other liabilities, current portion:
Foreign currency forward contracts	$	(769	)	$	—	$	(769	)	$	—
Other liabilities, excluding current portion:
Foreign currency forward contracts	(132		)	—		(132		)	—
Total financial liabilities	$	(901	)	$	—	$	(901	)	$	—

Marketable Securities (Tables)

9 Months Ended

Sep. 30, 2016

Cash and Cash Equivalents [Abstract]

Summary of cash, cash equivalents and marketable securities

A summary of the Company’s cash, cash equivalents and marketable securities is shown below:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
As of September 30, 2016
Cash and cash equivalents:
Cash and money market funds	$	719,692	$	—	$	—		$	719,692
Total cash and cash equivalents	$	719,692	$	—	$	—		$	719,692
Marketable securities:
Government-sponsored enterprise securities (due within 1 year)	130,404		29		(2		)	130,431
Commercial paper (due within 1 year)	131,099		277		—			131,376
Corporate debt securities (due within 1 year)	147,016		6		(80		)	146,942
Total marketable securities	$	408,519	$	312	$	(82	)	$	408,749
Total cash, cash equivalents and marketable securities	$	1,128,211	$	312	$	(82	)	$	1,128,441

As of December 31, 2015
Cash and cash equivalents:
Cash and money market funds	$	582,352	$	—	$	—		$	582,352
Government-sponsored enterprise securities	85,994		—		—			85,994
Commercial paper	34,889		—		—			34,889
Corporate debt securities	11,533		—		—			11,533
Total cash and cash equivalents	$	714,768	$	—	$	—		$	714,768
Marketable securities:
Government-sponsored enterprise securities (due within 1 year)	$	87,176	$	—	$	(14	)	$	87,162
Commercial paper (due within 1 year)	98,877		246		—			99,123
Corporate debt securities (due within 1 year)	141,515		—		(106		)	141,409
Total marketable securities	$	327,568	$	246	$	(120	)	$	327,694
Total cash, cash equivalents and marketable securities	$	1,042,336	$	246	$	(120	)	$	1,042,462

Accumulated Other Comprehensive (Loss) Income (Tables)

9 Months Ended

Sep. 30, 2016

Equity [Abstract]

Accumulated Other Comprehensive (Loss) Income

A summary of the Company's changes in accumulated other comprehensive (loss) income by component is shown below:



	Foreign Currency Translation Adjustment			Unrealized Holding Gains on Marketable Securities		Unrealized Gains (Losses) on Foreign Currency Forward Contracts, net of tax			Total
	(in thousands)
Balance at December 31, 2015	$	(2,080	)	$	126	$	3,778		$	1,824
Other comprehensive (loss) income before reclassifications	(7,709		)	104		6,715			(890		)
Amounts reclassified from accumulated other comprehensive loss	—			—		(4,779		)	(4,779		)
Net current period other comprehensive (loss) income	$	(7,709	)	$	104	$	1,936		$	(5,669	)
Balance at September 30, 2016	$	(9,789	)	$	230	$	5,714		$	(3,845	)



	Foreign Currency Translation Adjustment			Unrealized Holding (Losses) Gains on Marketable Securities			Unrealized Gains (Losses) on Foreign Currency Forward Contracts			Total
	(in thousands)
Balance at December 31, 2014	$	(971	)	$	(123	)	$	2,011		$	917
Other comprehensive (loss) income before reclassifications	(164		)	186			4,072			4,094
Amounts reclassified from accumulated other comprehensive loss	—			—			(3,500		)	(3,500		)
Net current period other comprehensive (loss) income	$	(164	)	$	186		$	572		$	594
Balance at September 30, 2015	$	(1,135	)	$	63		$	2,583		$	1,511

Hedging (Tables)

9 Months Ended

Sep. 30, 2016

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Schedule of Cash Flow Hedging Instruments

The following table summarizes the notional amount of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges:



	As of September 30, 2016		As of December 31, 2015
Foreign Currency	(in thousands)
Euro	$	156,245	$	103,362
British pound sterling	73,684		78,756
Australian dollar	26,550		27,167
Total foreign currency forward contracts	$	256,479	$	209,285

Schedule of Foreign Exchange Contracts



As of September 30, 2016
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid and other current assets	$	7,644	Other liabilities, current portion	$	(1,459	)
Other assets	217		Other liabilities, excluding current portion	(315		)
Total assets	$	7,861	Total liabilities	$	(1,774	)



As of December 31, 2015
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid and other current assets	$	5,161	Other liabilities, current portion	$	(769	)
Other assets	605		Other liabilities, excluding current portion	(132		)
Total assets	$	5,766	Total liabilities	$	(901	)

Derivatives Offsetting

The following table summarizes the potential effect of offsetting derivatives by type of financial instrument on the Company's condensed consolidated balance sheets:



	As of September 30, 2016
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	7,861		$	—	$	7,861		$	(1,774	)	$	6,087
Total liabilities	$	(1,774	)	$	—	$	(1,774	)	$	1,774		$	—



	As of December 31, 2015
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	5,766		$	—	$	5,766		$	(901	)	$	4,865
Total liabilities	$	(901	)	$	—	$	(901	)	$	901		$	—

Inventories (Tables)

9 Months Ended

Sep. 30, 2016

Inventory Disclosure [Abstract]

Schedule of Inventories by Type

Inventories consisted of the following:



	As of September 30, 2016		As of December 31, 2015
	(in thousands)
Raw materials	$	9,824	$	8,696
Work-in-process	46,057		40,695
Finished goods	15,918		7,816
Total	$	71,799	$	57,207

Stock-based Compensation Expense (Tables)

9 Months Ended

Sep. 30, 2016

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Stock-based compensation expense by line item

During the three and nine months ended September 30, 2016 and 2015, the Company recognized the following stock-based compensation expense:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Stock-based compensation expense by type of award:
Stock options	$	28,773		$	39,074		$	86,859		$	105,720
Restricted stock and restricted stock units	30,966			26,203			88,107			78,274
ESPP share issuances	2,425			1,738			6,385			5,703
Less stock-based compensation expense capitalized to inventories	(955		)	(1,281		)	(2,728		)	(3,318		)
Total stock-based compensation included in costs and expenses	$	61,209		$	65,734		$	178,623		$	186,379

Stock-based compensation expense by line item:
Research and development expenses	$	39,980		$	44,701		$	115,068		$	124,550
Sales, general and administrative expenses	21,229			21,033			63,555			61,829
Total stock-based compensation included in costs and expenses	$	61,209		$	65,734		$	178,623		$	186,379

Unrecognized stock-based compensation expense, net of estimated forfeitures



	As of September 30, 2016
	Unrecognized Expense, Net of Estimated Forfeitures		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Stock options	$	185,148	2.66
Restricted stock and restricted stock units	$	206,336	2.57
ESPP share issuances	$	2,886	0.47

Stock options outstanding and exercisable

The following table summarizes information about stock options outstanding and exercisable at September 30, 2016:



	Options Outstanding				Options Exercisable
Range of Exercise Prices	Number Outstanding	Weighted-average Remaining Contractual Life	Weighted-average Exercise Price		Number Exercisable	Weighted-average Exercise Price
	(in thousands)	(in years)	(per share)		(in thousands)	(per share)
$18.93–$20.00	137	1.35	$	18.93	137	$	18.93
$20.01–$40.00	1,816	3.32	$	34.08	1,815	$	34.07
$40.01–$60.00	1,937	5.89	$	48.19	1,719	$	48.57
$60.01–$80.00	1,348	7.38	$	75.90	809	$	75.51
$80.01–$100.00	4,598	8.74	$	90.62	1,271	$	89.38
$100.01–$120.00	1,627	8.33	$	109.33	606	$	109.29
$120.01–$134.69	1,484	8.80	$	130.60	510	$	130.06
Total	12,947	7.29	$	80.99	6,867	$	66.29

Restructuring Liabilities (Tables)

9 Months Ended

Sep. 30, 2016

Kendall Restructuring

Restructuring Cost and Reserve [Line Items]

The activities related to the restructuring liability for the three and nine months ended September 30, 2016 and 2015 were as follows:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Liability, beginning of the period	$	6,388		$	9,924		$	7,944		$	11,596
Cash payments	(5,340		)	(3,975		)	(13,104		)	(10,544		)
Cash received from subleases	2,866			2,919			8,882			8,194
Restructuring expense (income)	30			146			222			(232		)
Liability, end of the period	$	3,944		$	9,014		$	3,944		$	9,014

Fan Pier Move Restructuring

Restructuring Cost and Reserve [Line Items]

The activities related to the restructuring liability for the three and nine months ended September 30, 2016 and 2015 were as follows:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Liability, beginning of the period	$	4,863		$	9,017		$	5,964		$	33,390
Cash payments	(4,199		)	(3,070		)	(10,451		)	(25,421		)
Cash received from subleases	2,539			1,820			7,308			1,820
Restructuring expense (income)	90			51			472			(1,971		)
Liability, end of the period	$	3,293		$	7,818		$	3,293		$	7,818

Other Restructuring

Restructuring Cost and Reserve [Line Items]

The activities related to the Company's other restructuring liabilities for the three and nine months ended September 30, 2016 and 2015 were as follows:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
	(in thousands)
Liability, beginning of the period	$	1,233		$	902		$	1,450		$	869
Cash payments	(1,121		)	(1,559		)	(1,794		)	(2,782		)
Restructuring expense	(112		)	1,629			344			2,885
Liability, end of the period	$	—		$	972		$	—		$	972

Basis of Presentation and Accounting Policies (Details)	9 Months Ended
Basis of Presentation and Accounting Policies (Details)	Sep. 30, 2016 segment
Accounting Policies [Abstract]
Number of operating segments	1

Product Revenues, Net (Details) $ in Thousands	9 Months Ended
Product Revenues, Net (Details) $ in Thousands	Sep. 30, 2016 USD ($)
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	$ 49,296
Provision related to current period sales	120,100
Adjustments related to prior period sales	(1,448)
Credits/payments made	(91,175)
Balance at September 30, 2016	76,773
Trade Allowances
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	2,089
Provision related to current period sales	14,680
Adjustments related to prior period sales	(82)
Credits/payments made	(14,505)
Balance at September 30, 2016	2,182
Rebates, Chargebacks and Discounts
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	44,669
Provision related to current period sales	98,242
Adjustments related to prior period sales	(1,081)
Credits/payments made	(70,718)
Balance at September 30, 2016	71,112
Product Returns
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	1,228
Provision related to current period sales	1,631
Adjustments related to prior period sales	(205)
Credits/payments made	(345)
Balance at September 30, 2016	2,309
Other Incentives
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	1,310
Provision related to current period sales	5,547
Adjustments related to prior period sales	(80)
Credits/payments made	(5,607)
Balance at September 30, 2016	$ 1,170

Collaborative Arrangements - Cystic Fibrosis Foundation Therapeutics Incorporated (Details) - USD ($)		3 Months Ended				9 Months Ended
	Oct. 13, 2016	Sep. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenues		$ 259,000			$ 1,546,000	$ 1,008,000	$ 2,999,000
Cystic Fibrosis Foundation Therapeutics Incorporated
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone Payments				$ 13,900,000
Milestone Revenues			$ 13,900,000
Additional Milestone Payments						$ 0
Subsequent Event \| Cystic Fibrosis Foundation Therapeutics Incorporated
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative funding	$ 75,000,000.0
Additional Collaborative Funding	$ 6,000,000.0

Collaborative Arrangements - CRISPR Therapeutics AG (Details) - CRISPR Therapeutics	1 Months Ended		3 Months Ended
	Oct. 31, 2016 USD ($)	Oct. 31, 2015 USD ($) target	Jun. 30, 2016 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Right to license, number of targets (up to) \| target		6
Up-front payment		$ 75,000,000
Investment in collaborative partner, pursuant to convertible loan agreement		30,000,000	$ 3,100,000
Collaborative funding		75,000,000
Collaborative arrangement development and regulatory potential milestone payments maximum		$ 420,000,000
Prior to marketing approval, time period of notice required to terminate (in days)		90 days
Subsequent to marketing approval, time period of notice required to terminate (in days)		270 days
Subsequent Event
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Investment in collaborative partner, pursuant to convertible loan agreement	$ 10,000,000

Collaborative Arrangements - Parion Sciences, Inc. (Details) - USD ($)		1 Months Ended
	Jun. 04, 2015	Jun. 30, 2015	Sep. 30, 2016	Dec. 31, 2015
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net [Abstract]
Intangible assets			$ 284,340,000	$ 284,340,000
Deferred tax liability, net			(133,270,000)	(110,439,000)
Goodwill			$ 50,384,000	$ 50,384,000
Parion Sciences, Inc
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Business Acquisition Contingent Consideration Commercial Milestones And Royalties Discount Rate	6.60%
Prior to marketing approval, time period of notice required to terminate (in days)		90 days
Subsequent to marketing approval, time period of notice required to terminate (in days)		180 days
Change of control prior to clinical trial, time period of notice required to terminate (in days)		30 days
Term of agreement following first commercial sale (in years)		10 years
Business Acquisition Contingent Consideration Development Milestones Discount Rate Low End Of Range	4.10%
Business Acquisition Contingent Consideration Development Milestones Discount Rate High End Of Range	5.90%
Business Combination, Consideration Transferred [Abstract]
Up-front payment	$ 80,000,000	$ 80,000,000
Business Combination, Liabilities Arising from Contingencies, Amount Recognized	175,340,000
Business Combination, Consideration Transferred	255,340,000
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net [Abstract]
Intangible assets	255,340,000	255,300,000
Business Combination, Recognized Identifiable Assets Acquired, Goodwill, and Liabilities Assumed, Net	(164,317,000)
Deferred tax liability, net	(91,023,000)
Other Liabilities Assets Net	(10,468,000)
Goodwill	$ 10,468,000
ENaC Inhibitors in CF \| Parion Sciences, Inc
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum		490,000,000
Collaborative arrangement regulatory potential milestone payments maximum, global filling and approval		360,000,000
Enac Inhibitors in Non Cf \| Parion Sciences, Inc
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum		370,000,000
Additional Enac Inhibitors \| Parion Sciences, Inc
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum		$ 230,000,000

Collaborative Arrangements - BioAxone Biosciences, Inc. (Details) - BioAxone Biosciences Inc - USD ($)	1 Months Ended	3 Months Ended
	Oct. 31, 2014	Dec. 31, 2014
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Up-front payment		$ 10,000,000
Maximum license fees and milestone payments	$ 90,000,000.0
In-process research and development intangible asset	29,000,000
Deferred tax liability attributable to BioAxone	$ 11,300,000
Purchase option, term of extension of expiration date (in years)	1 year

Collaborative Arrangements - Aggregate VIE Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015	Jun. 30, 2015	Jun. 04, 2015
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
(Benefit from) provision for income taxes	$ (503)	$ (1,330)	$ (24,118)	$ (31,760)
Net (income) loss attributable to noncontrolling interest	696	(1,333)	(33,207)	30,909
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Restricted cash and cash equivalents (VIE)	58,420		58,420		$ 78,910
Prepaid expenses and other current assets	61,012		61,012		54,736
Intangible assets	284,340		284,340		284,340
Goodwill	50,384		50,384		50,384
Other assets	10,002		10,002		6,912
Accounts payable	50,914		50,914		74,942
Other current liabilities	292,015		292,015		305,820
Deferred tax liability, net	133,270		133,270		110,439
Other liabilities	30,524		30,524		31,778
Noncontrolling interest	186,795		186,795		153,661
BioAxone Biosciences Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Contingent consideration, liability	28,800		28,800		28,000
Parion Sciences, Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
(Benefit from) provision for income taxes	(500)		(20,100)
Contingent consideration, liability	232,500		232,500		179,000
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Intangible assets						$ 255,300	$ 255,340
Goodwill							10,468
Deferred tax liability, net							$ 91,023
Variable Interest Entity, Primary Beneficiary
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Loss attributable to noncontrolling interest before provision for income taxes	2,406	1,743	6,080	3,322
(Benefit from) provision for income taxes	(510)	777	20,063	30,367
(Increase) decrease in fair value of contingent milestone and royalty payments	(1,200)	(3,853)	(59,350)	(2,780)
Net (income) loss attributable to noncontrolling interest	696	(1,333)	(33,207)	30,909
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Restricted cash and cash equivalents (VIE)	58,420		58,420		78,910
Prepaid expenses and other current assets	2,360		2,360		3,138
Intangible assets	284,340		284,340		284,340
Goodwill	19,391		19,391		19,391
Other assets	382		382		455
Accounts payable	1,122		1,122		676
Taxes payable	6,263		6,263		24,554
Other current liabilities	1,121		1,121		7,100
Deferred tax liability, net	133,270		133,270		110,438
Other liabilities	300		300		300
Noncontrolling interest	186,795		186,795		$ 153,661
Variable Interest Entity, Primary Beneficiary \| BioAxone Biosciences Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
(Increase) decrease in fair value of contingent milestone and royalty payments	(100)	628	(850)	80
Variable Interest Entity, Primary Beneficiary \| Parion Sciences, Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
(Increase) decrease in fair value of contingent milestone and royalty payments	$ (1,100)	$ (4,481)	$ (58,500)	$ (2,860)

Collaborative Arrangements - Janssen Pharmaceuticals, Inc. (Details) - Janssen - USD ($) $ in Millions	3 Months Ended		9 Months Ended		12 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2014
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Up-front payment					$ 35.0
Time period of notice required to terminate			6 months
Reimbursement for development and commercialization of compounds	$ 2.8	$ 4.0	$ 10.6	$ 18.7

Collaborative Arrangements - Moderna Therapeutics, Inc. (Details) - Moderna Therapeutics, Inc. $ in Millions	1 Months Ended
	Jul. 31, 2016 USD ($)
Schedule of Collaborative Arrangement Agreements [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum	$ 275.0
Collaborative Arrangement Approval and Reimbursement Milestones	220.0
Collaborative Arrangement, Investment in Collaborative Partner, Amount	20.0
Collaborative Arrangement Up-front License Fee	$ 20.0

Earnings Per Share (Details) - shares shares in Thousands	3 Months Ended		9 Months Ended
Earnings Per Share (Details) - shares shares in Thousands	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	12,947	12,025	12,947	12,025
Unvested restricted stock and restricted stock units
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	3,624	3,367	3,624	3,367

Fair Value Measurements (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Level 3
Financial instruments carried at fair value (liability position):
Term loan fair value	$ 297,800
Recurring basis
Financial assets carried at fair value:
Total financial assets	518,454	$ 665,383
Financial instruments carried at fair value (liability position):
Total financial liabilities	1,774	901
Recurring basis \| Money market funds
Financial assets carried at fair value:
Cash equivalents	101,844	199,507
Recurring basis \| Commercial paper
Financial assets carried at fair value:
Cash equivalents		34,889
Marketable securities	131,376	99,123
Recurring basis \| Government-sponsored enterprise securities
Financial assets carried at fair value:
Cash equivalents		85,994
Marketable securities	130,431	87,162
Recurring basis \| Corporate debt securities
Financial assets carried at fair value:
Cash equivalents		11,533
Marketable securities	146,942	141,409
Recurring basis \| Level 1
Financial assets carried at fair value:
Total financial assets	232,275	372,663
Financial instruments carried at fair value (liability position):
Total financial liabilities	0	0
Recurring basis \| Level 1 \| Money market funds
Financial assets carried at fair value:
Cash equivalents	101,844	199,507
Recurring basis \| Level 1 \| Commercial paper
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis \| Level 1 \| Government-sponsored enterprise securities
Financial assets carried at fair value:
Cash equivalents		85,994
Marketable securities	130,431	87,162
Recurring basis \| Level 1 \| Corporate debt securities
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis \| Level 2
Financial assets carried at fair value:
Total financial assets	286,179	292,720
Financial instruments carried at fair value (liability position):
Total financial liabilities	1,774	901
Recurring basis \| Level 2 \| Money market funds
Financial assets carried at fair value:
Cash equivalents	0	0
Recurring basis \| Level 2 \| Commercial paper
Financial assets carried at fair value:
Cash equivalents		34,889
Marketable securities	131,376	99,123
Recurring basis \| Level 2 \| Government-sponsored enterprise securities
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis \| Level 2 \| Corporate debt securities
Financial assets carried at fair value:
Cash equivalents		11,533
Marketable securities	146,942	141,409
Recurring basis \| Level 3
Financial assets carried at fair value:
Total financial assets	0	0
Financial instruments carried at fair value (liability position):
Total financial liabilities	0	0
Recurring basis \| Level 3 \| Money market funds
Financial assets carried at fair value:
Cash equivalents	0	0
Recurring basis \| Level 3 \| Commercial paper
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis \| Level 3 \| Government-sponsored enterprise securities
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis \| Level 3 \| Corporate debt securities
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Prepaid and other current assets \| Foreign currency forward contracts \| Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	7,644	5,161
Prepaid and other current assets \| Foreign currency forward contracts \| Recurring basis \| Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0	0
Prepaid and other current assets \| Foreign currency forward contracts \| Recurring basis \| Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	7,644	5,161
Prepaid and other current assets \| Foreign currency forward contracts \| Recurring basis \| Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0	0
Other Assets \| Foreign currency forward contracts \| Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	217	605
Other Assets \| Foreign currency forward contracts \| Recurring basis \| Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0	0
Other Assets \| Foreign currency forward contracts \| Recurring basis \| Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	217	605
Other Assets \| Foreign currency forward contracts \| Recurring basis \| Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0	0
Other liabilities, current portion \| Foreign currency forward contracts \| Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	(1,459)
Financial instruments carried at fair value (liability position):
Derivative liability current		(769)
Other liabilities, current portion \| Foreign currency forward contracts \| Recurring basis \| Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0
Financial instruments carried at fair value (liability position):
Derivative liability current		0
Other liabilities, current portion \| Foreign currency forward contracts \| Recurring basis \| Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	(1,459)
Financial instruments carried at fair value (liability position):
Derivative liability current		(769)
Other liabilities, current portion \| Foreign currency forward contracts \| Recurring basis \| Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0
Financial instruments carried at fair value (liability position):
Derivative liability current		0
Other liabilities, excluding current portion \| Foreign currency forward contracts \| Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	(315)
Financial instruments carried at fair value (liability position):
Derivative liability noncurrent		(132)
Other liabilities, excluding current portion \| Foreign currency forward contracts \| Recurring basis \| Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0
Financial instruments carried at fair value (liability position):
Derivative liability noncurrent		0
Other liabilities, excluding current portion \| Foreign currency forward contracts \| Recurring basis \| Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	(315)
Financial instruments carried at fair value (liability position):
Derivative liability noncurrent		(132)
Other liabilities, excluding current portion \| Foreign currency forward contracts \| Recurring basis \| Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0
Financial instruments carried at fair value (liability position):
Derivative liability noncurrent		$ 0
Variable Interest Entity, Primary Beneficiary \| BioAxone Biosciences Inc \| Level 1
Financial instruments carried at fair value (liability position):
Cash and cash equivalents	$ 57,900

Marketable Securities (Details) - USD ($)	3 Months Ended	9 Months Ended
Marketable Securities (Details) - USD ($)	Sep. 30, 2016	Sep. 30, 2016	Dec. 31, 2015
Summary of cash, cash equivalents and marketable securities
Other than Temporary Impairment Losses, Investments	$ 0	$ 0
Amortized Cost	1,128,211,000	1,128,211,000	$ 1,042,336,000
Gross Unrealized Gains	312,000	312,000	246,000
Gross Unrealized Losses	(82,000)	(82,000)	(120,000)
Fair Value	1,128,441,000	1,128,441,000	1,042,462,000
Available-for-sale Securities, Gross Realized Gains (Losses), Sale Proceeds	0	0
Total cash and cash equivalents
Summary of cash, cash equivalents and marketable securities
Amortized Cost	719,692,000	719,692,000	714,768,000
Gross Unrealized Gains	0	0	0
Gross Unrealized Losses	0	0	0
Fair Value	719,692,000	719,692,000	714,768,000
Cash and money market funds
Summary of cash, cash equivalents and marketable securities
Amortized Cost	719,692,000	719,692,000	582,352,000
Gross Unrealized Gains	0	0	0
Gross Unrealized Losses	0	0	0
Fair Value	719,692,000	719,692,000	582,352,000
Government-sponsored enterprise securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost			85,994,000
Gross Unrealized Gains			0
Gross Unrealized Losses			0
Fair Value			85,994,000
Commercial paper
Summary of cash, cash equivalents and marketable securities
Amortized Cost			34,889,000
Gross Unrealized Gains			0
Gross Unrealized Losses			0
Fair Value			34,889,000
Corporate debt securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost			11,533,000
Gross Unrealized Gains			0
Gross Unrealized Losses			0
Fair Value			11,533,000
Total marketable securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost	408,519,000	408,519,000	327,568,000
Gross Unrealized Gains	312,000	312,000	246,000
Gross Unrealized Losses	(82,000)	(82,000)	(120,000)
Fair Value	408,749,000	408,749,000	327,694,000
Government-sponsored enterprise securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	130,404,000	130,404,000	87,176,000
Gross Unrealized Gains	29,000	29,000	0
Gross Unrealized Losses	(2,000)	(2,000)	(14,000)
Fair Value	130,431,000	130,431,000	87,162,000
Commercial paper (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	131,099,000	131,099,000	98,877,000
Gross Unrealized Gains	277,000	277,000	246,000
Gross Unrealized Losses	0	0	0
Fair Value	131,376,000	131,376,000	99,123,000
Corporate debt securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	147,016,000	147,016,000	141,515,000
Gross Unrealized Gains	6,000	6,000	0
Gross Unrealized Losses	(80,000)	(80,000)	(106,000)
Fair Value	$ 146,942,000	$ 146,942,000	$ 141,409,000

Accumulated Other Comprehensive (Loss) Income (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at balance sheet date			$ 1,824	$ 917
Other comprehensive (loss) income before reclassifications			(890)	4,094
Amounts reclassified from accumulated other comprehensive loss			(4,779)	(3,500)
Total changes in other comprehensive loss	$ (455)	$ 3,218	(5,669)	594
Balance at balance sheet date	(3,845)	1,511	(3,845)	1,511
Foreign Currency Translation Adjustment
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at balance sheet date			(2,080)	(971)
Other comprehensive (loss) income before reclassifications			(7,709)	(164)
Amounts reclassified from accumulated other comprehensive loss			0	0
Total changes in other comprehensive loss			(7,709)	(164)
Balance at balance sheet date	(9,789)	(1,135)	(9,789)	(1,135)
Unrealized Holding Gains on Marketable Securities
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at balance sheet date			126	(123)
Other comprehensive (loss) income before reclassifications			104	186
Amounts reclassified from accumulated other comprehensive loss			0	0
Total changes in other comprehensive loss			104	186
Balance at balance sheet date	230	63	230	63
Unrealized Gains (Losses) on Foreign Currency Forward Contracts, net of tax
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at balance sheet date			3,778	2,011
Other comprehensive (loss) income before reclassifications			6,715	4,072
Amounts reclassified from accumulated other comprehensive loss			(4,779)	(3,500)
Total changes in other comprehensive loss			1,936	572
Balance at balance sheet date	$ 5,714	$ 2,583	$ 5,714	$ 2,583

Hedging (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
Hedging (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Sep. 30, 2016	Dec. 31, 2015
Derivative [Line Items]
Amount of Ineffectiveness on Net Investment Hedges	$ 0	$ 0
Offsetting Derivative Assets [Abstract]
Gross Amounts Recognized	7,861	7,861	$ 5,766
Gross Amounts Offset	0	0	0
Gross Amounts Presented	7,861	7,861	5,766
Gross Amounts Not Offset	(1,774)	(1,774)	(901)
Legal Offset	6,087	6,087	4,865
Offsetting Derivative Liabilities [Abstract]
Gross Amounts Recognized	(1,774)	(1,774)	(901)
Gross Amounts Offset	0	0	0
Gross Amounts Presented	(1,774)	(1,774)	(901)
Gross Amounts Not Offset	1,774	1,774	901
Legal Offset	0	0	0
Prepaid and other current assets
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets	7,644	7,644	5,161
Other liabilities, current portion
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - liabilities	(1,459)	(1,459)	(769)
Other assets
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets	217	217	605
Other liabilities, excluding current portion
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - liabilities	(315)	(315)	(132)
Designated as hedging instrument \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	256,479	256,479	209,285
Designated as hedging instrument \| Euro \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	156,245	156,245	103,362
Designated as hedging instrument \| British pound sterling \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	73,684	73,684	78,756
Designated as hedging instrument \| Australian dollar \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	$ 26,550	$ 26,550	$ 27,167
Minimum \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Derivative term		1 month
Maximum \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Derivative term		18 months

Inventories - Schedule of Inventories (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Inventory Disclosure [Abstract]
Raw materials	$ 9,824	$ 8,696
Work-in-process	46,057	40,695
Finished goods	15,918	7,816
Total	$ 71,799	$ 57,207

Intangible Assets and Goodwill (Details) - USD ($) $ in Thousands	1 Months Ended
	Oct. 31, 2014	Sep. 30, 2016	Dec. 31, 2015	Jun. 30, 2015	Jun. 04, 2015
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets		$ 284,340	$ 284,340
Goodwill		50,384	50,384
Parion Sciences, Inc
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets				$ 255,300	$ 255,340
Goodwill					$ 10,468
BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
In-process research and development intangible asset	$ 29,000
Variable Interest Entity, Primary Beneficiary
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets		284,340	284,340
Goodwill		$ 19,391	$ 19,391
Variable Interest Entity, Primary Beneficiary \| BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
In-process research and development intangible asset	$ 29,000
Indefinite-lived Intangible Assets \| Variable Interest Entity, Primary Beneficiary \| Parion Sciences, Inc
Indefinite-Lived Intangible Assets [Line Items]
Fair value inputs, discount rate (percent)	7.10%
Indefinite-lived Intangible Assets \| Variable Interest Entity, Primary Beneficiary \| BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
Fair value inputs, discount rate (percent)	7.50%

Long-term Obligations - Fan Pier Leases (Details) $ in Thousands, ft² in Millions	12 Months Ended
	Dec. 31, 2011 ft² lease building	Sep. 30, 2016 USD ($)	Dec. 31, 2015 USD ($)
Property, Plant and Equipment [Line Items]
Property and equipment, net		$ 687,613	$ 697,715
Fan Pier Leases
Property, Plant and Equipment [Line Items]
Number of leases \| lease	2
Area of real estate property (in square feet) \| ft²	1.1
Number of buildings under lease agreement \| building	2
Optional term of lease agreement (in years)	10 years
Fan Pier Leases \| Buildings
Property, Plant and Equipment [Line Items]
Construction financing lease obligation, current and noncurrent		472,700	473,000
Fan Pier Leases \| Construction in progress
Property, Plant and Equipment [Line Items]
Property and equipment, net		$ 492,300	$ 502,300

Long-term Obligations - San Diego Lease (Details) - San Diego Lease $ in Millions	Dec. 02, 2015 USD ($) ft² term_extension
Property, Plant and Equipment [Line Items]
Area of real estate property (in square feet) \| ft²	170,000
Length of lease	16 years
Average yearly aggregate rent \| $	$ 10.2
Amount of optional renewal terms \| term_extension	2
Optional renewal term length	5 years

Long-term Obligations - Term Loan (Details) - Senior Secured Term Loan - USD ($)	1 Months Ended
	Oct. 31, 2016	Jul. 31, 2014	Sep. 30, 2016	Dec. 31, 2015
Debt Instrument [Line Items]
Face amount of term loan		$ 300,000,000
Interest rate, stated percentage		7.20%
Unamortized discount on term loan		$ 5,300,000	$ 2,100,000	$ 4,600,000
Minimum
Debt Instrument [Line Items]
Interest rate, stated percentage		6.20%
Minimum \| LIBOR
Debt Instrument [Line Items]
Basis spread on variable rate (percent)		5.00%
Subsequent Event
Debt Instrument [Line Items]
Repayments of Debt	$ 300,000,000.0
Gain (Loss) on Extinguishment of Debt	$ 2,200,000

Long-term Obligations - Credit Facility (Details) - Subsequent Event	Oct. 13, 2016 USD ($)
Line of Credit Facility [Line Items]
Line of Credit Facility, Fair Value of Amount Outstanding	$ 300,000,000.0
Line Of Credit Facility Additional Borrowing Capacity	300,000,000.0
Line of Credit
Line of Credit Facility [Line Items]
Line of Credit Facility, Current Borrowing Capacity	500,000,000.0
Debt Covenant, Minimum Consolidated EBITDA	$ 200,000,000.0
Debt Covenant, Consolidated Leverage Ratio	3.00%
Base Rate \| Minimum \| Line of Credit
Line of Credit Facility [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	0.75%
Base Rate \| Maximum \| Line of Credit
Line of Credit Facility [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	1.50%
Eurodollar \| Minimum \| Line of Credit
Line of Credit Facility [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	1.75%
Eurodollar \| Maximum \| Line of Credit
Line of Credit Facility [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	2.50%

Stock-based Compensation Expense - (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Stock-based compensation expense:
Less stock-based compensation expense capitalized to inventories	$ (955)	$ (1,281)	$ (2,728)	$ (3,318)
Total stock-based compensation included in costs and expenses	61,209	65,734	178,623	186,379
Stock options
Stock-based compensation expense:
Stock-based compensation expense by type of award:	28,773	39,074	86,859	105,720
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	185,148		$ 185,148
Weighted-average recognition period (in years)			2 years 7 months 28 days
Restricted stock and restricted stock units
Stock-based compensation expense:
Stock-based compensation expense by type of award:	30,966	26,203	$ 88,107	78,274
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	206,336		$ 206,336
Weighted-average recognition period (in years)			2 years 6 months 26 days
ESPP share issuances
Stock-based compensation expense:
Stock-based compensation expense by type of award:	2,425	1,738	$ 6,385	5,703
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	2,886		$ 2,886
Weighted-average recognition period (in years)			5 months 19 days
Research and development expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	39,980	44,701	$ 115,068	124,550
Sales, general and administrative expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	$ 21,229	$ 21,033	$ 63,555	$ 61,829

Stock-based Compensation Expense - Stock Options Outstanding and Exercisable (Details) shares in Thousands	9 Months Ended
	Sep. 30, 2016 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price range, options outstanding (in shares) \| shares	12,947
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 3 months 15 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 80.99
Exercise price range, options exercisable (in shares) \| shares	6,867
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 66.29
$18.93–$20.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	18.93
Exercise price, high end of range (usd per share)	$ 20.00
Exercise price range, options outstanding (in shares) \| shares	137
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	1 year 4 months 6 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 18.93
Exercise price range, options exercisable (in shares) \| shares	137
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 18.93
$20.01–$40.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	20.01
Exercise price, high end of range (usd per share)	$ 40
Exercise price range, options outstanding (in shares) \| shares	1,816
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	3 years 3 months 26 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 34.08
Exercise price range, options exercisable (in shares) \| shares	1,815
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 34.07
$40.01–$60.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	40.01
Exercise price, high end of range (usd per share)	$ 60
Exercise price range, options outstanding (in shares) \| shares	1,937
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	5 years 10 months 21 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 48.19
Exercise price range, options exercisable (in shares) \| shares	1,719
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 48.57
$60.01–$80.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	60.01
Exercise price, high end of range (usd per share)	$ 80
Exercise price range, options outstanding (in shares) \| shares	1,348
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 4 months 17 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 75.90
Exercise price range, options exercisable (in shares) \| shares	809
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 75.51
$80.01–$100.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	80.01
Exercise price, high end of range (usd per share)	$ 100
Exercise price range, options outstanding (in shares) \| shares	4,598
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 8 months 27 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 90.62
Exercise price range, options exercisable (in shares) \| shares	1,271
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 89.38
$100.01–$120.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	100.01
Exercise price, high end of range (usd per share)	$ 120
Exercise price range, options outstanding (in shares) \| shares	1,627
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 3 months 29 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 109.33
Exercise price range, options exercisable (in shares) \| shares	606
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 109.29
$120.01–$134.69
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	120.01
Exercise price, high end of range (usd per share)	$ 134.69
Exercise price range, options outstanding (in shares) \| shares	1,484
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 9 months 18 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 130.60
Exercise price range, options exercisable (in shares) \| shares	510
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 130.06

Other Arrangements (Details) - USD ($)	12 Months Ended
Other Arrangements (Details) - USD ($)	Dec. 31, 2008	Sep. 30, 2016
Sale of HIV Protease Inhibitor Royalty Stream
Gross proceeds from sale of royalty rights receivable from GlaxoSmithKline	$ 160,000,000.0
Deferred revenue royalty purchase agreement		$ 15,800,000

Income Taxes (Details) - USD ($)	3 Months Ended		9 Months Ended		12 Months Ended
Income Taxes (Details) - USD ($)	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Schedule of Collaborative Arrangement Agreements [Line Items]
Provision for income taxes	$ 503,000	$ 1,330,000	$ 24,118,000	$ 31,760,000
Income Tax Liability Associated With Variable Interest Entity	0		0
Unrecognized tax benefits	0		0		$ 400,000
Income taxes, interest and penalties accrued	0		0
Income taxes, material interest or penalties related to uncertain tax positions			0		$ 0
Unrecognized Tax Benefits, Reduction Resulting from Lapse of Applicable Statute of Limitations	400,000
Parion Sciences, Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Provision for income taxes	$ 500,000		$ 20,100,000

Restructuring Liabilities - Narrative (Details)	3 Months Ended		12 Months Ended
Restructuring Liabilities - Narrative (Details)	Mar. 31, 2015 ft² lease	Sep. 30, 2014 facility	Dec. 31, 2003
Kendall Restructuring
Restructuring Cost and Reserve [Line Items]
Lease term (in years)			15 years
Restructuring and related activities, leased office space, maximum percentage used - not more than			50.00%
Fan Pier Move Restructuring
Restructuring Cost and Reserve [Line Items]
Number of facilities decommissioned \| facility		3
Number of leases terminated \| lease	2
Area of real estate property (in square feet) \| ft²	120,000
Discount rate related to leases (percent)	9.00%

Restructuring Liabilities - Activity Related to Restructuring Liability (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Restructuring activities
Restructuring expense (income)	$ 8	$ 1,826	$ 1,038	$ 682
Kendall Restructuring
Restructuring activities
Liability, beginning of the period	6,388	9,924	7,944	11,596
Cash payments	(5,340)	(3,975)	(13,104)	(10,544)
Cash received from subleases	2,866	2,919	8,882	8,194
Restructuring expense (income)	30	146	222	(232)
Liability, end of the period	3,944	9,014	3,944	9,014
Fan Pier Move Restructuring
Restructuring activities
Liability, beginning of the period	4,863	9,017	5,964	33,390
Cash payments	(4,199)	(3,070)	(10,451)	(25,421)
Cash received from subleases	2,539	1,820	7,308	1,820
Restructuring expense (income)	90	51	472	(1,971)
Liability, end of the period	3,293	7,818	3,293	7,818
Other Restructuring
Restructuring activities
Liability, beginning of the period	1,233	902	1,450	869
Cash payments	(1,121)	(1,559)	(1,794)	(2,782)
Restructuring expense (income)	(112)	1,629	344	2,885
Liability, end of the period	$ 0	$ 972	$ 0	$ 972

Commitments and Contingencies (Details) - USD ($)	Sep. 30, 2016	Dec. 31, 2015
Loss Contingencies [Line Items]
Contingent liabilities	$ 0	$ 0
Indemnification Claims	0
Restricted cash and cash equivalents	21,900,000
IBEW
Loss Contingencies [Line Items]
Legal reserves	$ 0