View Filing Data

Print Document View Excel Document

Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2014	Jul. 25, 2014
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	Jun. 30, 2014
Document Fiscal Year Focus	2014
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Common Stock, Shares Outstanding (shares)		238,081,533

Condensed Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Revenues:
Product revenues, net	$ 122,319	$ 254,789	$ 225,780	$ 522,170
Royalty revenues	13,015	49,120	23,748	92,693
Collaborative revenues	3,087	6,841	7,344	24,255
Total revenues	138,421	310,750	256,872	639,118
Costs and expenses:
Cost of product revenues	9,655	24,695	18,227	55,650
Royalty expenses	7,645	13,236	14,549	25,024
Research and development expenses	224,780	222,455	463,743	440,550
Sales, general and administrative expenses	77,446	106,521	151,658	199,400
Restructuring expenses	(270)	776	5,918	815
Intangible asset impairment charge	0	0	0	412,900
Total costs and expenses	319,256	367,683	654,095	1,134,339
Loss from operations	(180,835)	(56,933)	(397,223)	(495,221)
Interest expense, net	(15,585)	(6,551)	(31,302)	(10,016)
Other income (expense), net	37,731	(27)	38,182	(1,214)
Loss before provision for (benefit from) income taxes	(158,689)	(63,511)	(390,343)	(506,451)
Provision for (benefit from) income taxes	693	(1,799)	1,496	(132,112)
Net loss	(159,382)	(61,712)	(391,839)	(374,339)
Net loss attributable to noncontrolling interest (Alios)	0	4,547	0	9,158
Net loss attributable to Vertex	$ (159,382)	$ (57,165)	$ (391,839)	$ (365,181)
Net loss per share attributable to Vertex common shareholders:
Basic (usd per share)	$ (0.68)	$ (0.26)	$ (1.68)	$ (1.67)
Diluted (usd per share)	$ (0.68)	$ (0.26)	$ (1.68)	$ (1.67)
Shares used in per share calculations:
Basic (shares)	233,808	222,053	233,353	218,795
Diluted (shares)	233,808	222,053	233,353	218,795

Condensed Consolidated Statements of Comprehensive Income (Loss) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Comprehensive Income (Loss), Net of Tax, Including Portion Attributable to Noncontrolling Interest [Abstract]
Net loss	$ (159,382)	$ (61,712)	$ (391,839)	$ (374,339)
Changes in other comprehensive loss:
Unrealized holding gains (losses) on marketable securities	82	(170)	55	(159)
Unrealized losses on foreign currency forward contracts	(89)	0	(125)	0
Foreign currency translation adjustment	281	89	353	(521)
Total changes in other comprehensive loss	274	(81)	283	(680)
Comprehensive loss	(159,108)	(61,793)	(391,556)	(375,019)
Comprehensive loss attributable to noncontrolling interest (Alios)	0	4,547	0	9,158
Comprehensive loss attributable to Vertex	$ (159,108)	$ (57,246)	$ (391,556)	$ (365,861)

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2014	Dec. 31, 2013
Current assets:
Cash and cash equivalents	$ 420,558	$ 569,299
Marketable securities, available for sale	798,603	895,777
Accounts receivable, net	81,842	85,517
Inventories	11,982	14,147
Prepaid expenses and other current assets	34,399	23,836
Total current assets	1,347,384	1,588,576
Restricted cash	129	130
Property and equipment, net	730,000	696,911
Goodwill	30,992	30,992
Other assets	9,315	2,432
Total assets	2,117,820	2,319,041
Current liabilities:
Accounts payable	55,363	49,327
Accrued expenses	237,789	271,077
Deferred revenues, current portion	27,174	21,510
Accrued restructuring expenses, current portion	8,498	14,286
Capital lease obligations, current portion	19,707	16,893
Other liabilities, current portion	14,442	24,736
Total current liabilities	362,973	397,829
Deferred revenues, excluding current portion	38,105	49,459
Accrued restructuring expenses, excluding current portion	10,486	14,067
Capital lease obligations, excluding current portion	45,053	48,754
Construction financing lease obligation, excluding current portion	473,268	440,937
Other liabilities, excluding current portion	15,666	11,590
Total liabilities	945,551	962,636
Commitments and contingencies
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at June 30, 2014 and December 31, 2013	0	0
Common stock, $0.01 par value; 300,000,000 shares authorized at June 30, 2014 and December 31, 2013; 237,331,086 and 233,788,852 shares issued and outstanding at June 30, 2014 and December 31, 2013, respectively	2,347	2,320
Additional paid-in capital	5,528,679	5,321,286
Accumulated other comprehensive loss	(23)	(306)
Accumulated deficit	(4,358,734)	(3,966,895)
Total shareholders’ equity	1,172,269	1,356,405
Total liabilities and shareholders’ equity	$ 2,117,820	$ 2,319,041

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2014	Dec. 31, 2013
Statement of Financial Position [Abstract]
Preferred stock, par value (usd per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized (shares)	1,000,000	1,000,000
Preferred stock, shares issued (shares)	0	0
Preferred stock, shares outstanding (shares)	0	0
Common stock, par value (usd per share)	$ 0.01	$ 0.01
Common stock, shares authorized (shares)	300,000,000	300,000,000
Common stock, shares issued (shares)	237,331,086	233,788,852
Common stock, shares outstanding (shares)	237,331,086	233,788,852

Condensed Consolidated Statements of Shareholders' Equity and Noncontrolling Interest - USD ($) shares in Thousands, $ in Thousands	Total	Total Vertex Shareholders' Equity	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit	Noncontrolling Interest (Alios)	Redeemable Noncontrolling Interest (Alios)
Balance (shares) at Dec. 31, 2012			217,287
Balance at Dec. 31, 2012	$ 1,195,852	$ 999,180	$ 2,149	$ 4,519,448	$ (550)	$ (3,521,867)	$ 196,672	$ 38,530
Increase (Decrease) in Stockholders' Equity
Unrealized holding losses on marketable securities	(159)	(159)			(159)
Unrealized losses on foreign currency forward contracts	0
Foreign currency translation adjustment	(521)	(521)			(521)
Net loss	(374,339)	(365,181)				(365,181)	(9,158)
Issuance of common stock under benefit plans (shares)			6,614
Issuance of common stock under benefit plans	213,729	213,801	$ 68	213,733			(72)
Convertible senior subordinated notes (due 2015) conversion (shares)			8,276
Convertible senior subordinated notes (due 2015) conversion	402,265	402,265	$ 83	402,182
Stock-based compensation expense	73,306	73,068		73,068			238
Change in liquidation value of noncontrolling interest	(684)						(684)	684
Balance (shares) at Jun. 30, 2013			232,177
Balance at Jun. 30, 2013	1,509,449	1,322,453	$ 2,300	5,208,431	(1,230)	(3,887,048)	186,996	39,214
Balance (shares) at Dec. 31, 2013			233,789
Balance at Dec. 31, 2013	1,356,405	1,356,405	$ 2,320	5,321,286	(306)	(3,966,895)	0	0
Increase (Decrease) in Stockholders' Equity
Unrealized holding losses on marketable securities	55	55			55
Unrealized losses on foreign currency forward contracts	(125)	(125)			(125)
Foreign currency translation adjustment	353	353			353
Net loss	(391,839)	(391,839)				(391,839)
Issuance of common stock under benefit plans (shares)			3,542
Issuance of common stock under benefit plans	117,947	117,947	$ 27	117,920
Stock-based compensation expense	89,473	89,473		89,473
Balance (shares) at Jun. 30, 2014			237,331
Balance at Jun. 30, 2014	$ 1,172,269	$ 1,172,269	$ 2,347	$ 5,528,679	$ (23)	$ (4,358,734)	$ 0	$ 0

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013
Cash flows from operating activities:
Net loss	$ (391,839)	$ (374,339)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization expense	29,960	21,245
Stock-based compensation expense	89,024	72,625
Other non-cash based compensation expense	0	5,857
Intangible asset impairment charge	0	412,900
Deferred income taxes	0	(130,661)
Write-down of inventories to net realizable value	0	5,083
Other non-cash items, net	22	7,455
Changes in operating assets and liabilities:
Accounts receivable, net	2,518	(18,462)
Inventories	1,194	6,620
Prepaid expenses and other assets	(17,538)	(18,152)
Accounts payable	7,671	(53,374)
Accrued expenses and other liabilities	(9,459)	4,616
Accrued restructuring expense	(9,369)	(1,276)
Deferred revenues	(5,866)	(6,842)
Net cash used in operating activities	(303,682)	(66,705)
Cash flows from investing activities:
Purchases of marketable securities	(703,977)	(898,706)
Sales and maturities of marketable securities	801,206	830,906
Expenditures for property and equipment	(27,227)	(18,408)
Decrease in restricted cash and cash equivalents	1	31,812
Decrease in restricted cash and cash equivalents (Alios)	0	11,695
Decrease (increase) in deposits	(528)	414
Net cash used in (provided by) investing activities	69,475	(42,287)
Cash flows from financing activities:
Issuances of common stock from employee benefit plans	117,947	207,872
Payments to redeem secured notes (due 2015)	0	(158)
Payments on capital lease obligations	(11,884)	(12,246)
Payments on construction financing lease obligation	(30,292)	(44,115)
Payments returned related to construction financing lease obligation	8,050	0
Net cash provided by (used in) financing activities	83,821	151,353
Effect of changes in exchange rates on cash	1,645	(521)
Net (decrease) increase in cash and cash equivalents	(148,741)	41,840
Cash and cash equivalents—beginning of period	569,299	489,407
Cash and cash equivalents—end of period	420,558	531,247
Supplemental disclosure of cash flow information:
Cash paid for interest	31,933	7,142
Cash paid for income taxes	798	0
Conversion of convertible senior subordinated notes (due 2015) for common stock	0	399,842
Unamortized deferred debt issuance costs exchanged	0	4,230
Capitalization of construction in-process related to construction financing lease obligation	25,564	130,222
Assets acquired under capital lease	$ 8,985	$ 21,576

Basis of Presentation and Accounting Policies	6 Months Ended
Basis of Presentation and Accounting Policies	Jun. 30, 2014
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 and (ii) its wholly-owned subsidiaries. In addition, the condensed consolidated financial statements for the period from June 13, 2011 through December 31, 2013, reflect the operations of Alios BioPharma, Inc. (“Alios”), a collaborator that was a variable interest entity (a “VIE”) for which the Company was deemed under applicable accounting guidance to have a variable interest and be the primary beneficiary. As of December 31, 2013, the Company deconsolidated Alios, and the Company's consolidated balance sheets as of June 30, 2014 and December 31, 2013 exclude Alios. 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 June 30, 2014 and 2013. 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, 2013, which are contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2013 that was filed with the Securities and Exchange Commission (the “SEC”) on February 11, 2014 (the "2013 Annual Report on Form 10-K"). 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, noncontrolling interest (Alios), the consolidation and deconsolidation of a VIE, leases and the income tax provision. 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 2013 Annual Report on Form 10-K. Recent Accounting Pronouncements For a discussion of recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2013 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the six months ended June 30, 2014 that had a material effect on the Company's condensed consolidated financial statements. In the second quarter of 2014, the Financial Accounting Standards Board issued amended guidance applicable to revenue recognition that will be effective for the Company for the year ending December 31, 2017. The new guidance must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach. Early adoption is not permitted. The new guidance applies a more principles-based approach to recognizing revenue. The Company is evaluating the new guidance and the expected effect on the Company’s condensed consolidated financial statements.

Product Revenues, Net

6 Months Ended

Jun. 30, 2014

Product Revenues [Abstract]

Product Revenues, Net

The Company sells its products principally to a limited number of major and selected regional wholesalers and specialty pharmacy providers in North America as well as government-owned and supported customers in Europe (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 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 Customer's 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 incentives offered to certain indirect customers, including patients. 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 six months ended June 30, 2014:



	Trade Allowances			Rebates, Chargebacks and Discounts			Product Returns			Other Incentives			Total
	(in thousands)
Balance at December 31, 2013	$	1,535		$	68,244		$	15,799		$	1,555		$	87,133
Provision related to current period sales	4,513			26,464			379			859			32,215
Adjustments related to prior period sales	(8		)	3,861			4,124			1			7,978
Credits/payments made	(5,271		)	(57,617		)	(4,160		)	(1,586		)	(68,634		)
Balance at June 30, 2014	$	769		$	40,952		$	16,142		$	829		$	58,692

Collaborative Arrangements

6 Months Ended

Jun. 30, 2014

Collaborative Arrangements

Collaborative Arrangements

Janssen Pharmaceutica NV

In 2006, the Company entered into a collaboration agreement (the “Janssen NV Agreement”) with Janssen Pharmaceutica NV (“Janssen NV”) for the development, manufacture and commercialization of telaprevir, which Janssen NV began marketing under the brand name INCIVO in certain of its territories in September 2011. Under the Janssen NV Agreement, Janssen NV agreed to be responsible for 50% of the drug development costs incurred under the development program for the parties’ territories (North America for the Company, and the rest of the world, other than specified countries in Asia, for Janssen NV) and has exclusive rights to commercialize telaprevir in its territories including Europe, South America, the Middle East, Africa and Australia. In November 2013, the Company and Janssen NV amended the collaboration agreement (the "2013 Janssen NV Amendment").

Janssen NV made a $165.0 million up-front license payment to the Company in 2006. The Company amortized the up-front license payment over the Company’s estimated period of performance under the Janssen NV Agreement through November 2013. As of November 2013, the effective date of the 2013 Janssen NV Amendment, there was $32.1 million remaining in deferred revenues related to this up-front license payment.

Janssen NV paid the Company a tiered royalty averaging in the mid-20% range as a percentage of net sales of INCIVO in Janssen NV’s territories through 2013. Janssen NV was, and continues to be, responsible for certain third-party royalties on net sales of INCIVO in its territories.

Pursuant to the 2013 Janssen NV Amendment, (i) Janssen NV made a payment of $152.0 million to the Company in the fourth quarter of 2013; (ii) Janssen NV's obligations to pay the Company royalties on net sales of INCIVO (telaprevir) terminated after the fourth quarter of 2013; and (iii) Janssen NV received a fully-paid license to commercialize INCIVO in its territories, subject to the continued payment of certain third-party royalties on its net sales of INCIVO.

The Company determined that the 2013 Janssen NV Amendment was a material modification to the Janssen NV Agreement because there was a material change to the consideration and deliverables under the agreement and determined that there is one undelivered element under the Janssen NV Agreement, as amended, which is the continuation of certain telaprevir development activities. The Company recognized $182.4 million of collaborative revenues pursuant to the Janssen NV Agreement in the fourth quarter of 2013. This amount was primarily attributable to (i) the residual consideration received from Janssen NV, including the $152.0 million fourth quarter 2013 payment and the remaining deferred revenues related to the 2006 up-front payment, less (ii) the best estimate of selling price for the remaining telaprevir development activities. As of June 30, 2014, the remaining deferred revenue balance related to the Janssen NV collaboration was $4.2 million and will be recognized as collaborative revenues as telaprevir development program activities are completed. In addition to the collaborative revenues, the Company will continue to record royalty revenues and corresponding royalty expenses related to third-party royalties that Janssen NV remains responsible for based on INCIVO net sales.

The agreement will continue in effect until the expiration of Janssen NV’s third-party royalty obligations, which expire on a country-by-country basis on the later of (a) the last-to-expire patent covering INCIVO or (b) the last required payment by Janssen NV to the Company pursuant to the agreement. In the European Union, the Company has a patent covering the composition-of-matter of INCIVO that expires in 2026.

During the three and six months ended June 30, 2014 and 2013, the Company recognized the following revenues attributable to the Janssen NV collaboration:



	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
	(in thousands)
Royalty revenues (INCIVO)	$	5,698	$	44,070	$	10,633	$	83,114
Collaborative revenues:
Up-front and amendment payments revenues	$	—	$	3,107	$	—	$	6,214
Net reimbursement for telaprevir development costs	1,483		37		2,872		9
Reimbursement for manufacturing services	—		—		—		10,299
Total collaborative revenues attributable to the Janssen NV collaboration	$	1,483	$	3,144	$	2,872	$	16,522
Total revenues attributable to the Janssen NV collaboration	$	7,181	$	47,214	$	13,505	$	99,636

Mitsubishi Tanabe Pharma Corporation

The Company has a collaboration agreement (the “MTPC Agreement”) with Mitsubishi Tanabe Pharma Corporation ("Mitsubishi Tanabe") pursuant to which Mitsubishi Tanabe has a fully-paid license to manufacture and commercialize TELAVIC (the brand name under which Mitsubishi Tanabe is marketing telaprevir) in Japan and other specified countries in Asia. The Company recognized no collaborative revenues attributable to the Mitsubishi Tanabe collaboration in the three and six months ended June 30, 2014 and 2013.

Cystic Fibrosis Foundation Therapeutics Incorporated

In April 2011, the Company entered into an amendment (the “April 2011 Amendment”) to its existing collaboration agreement with Cystic Fibrosis Foundation Therapeutics Incorporated (“CFFT”) pursuant to which CFFT agreed to provide financial support for (i) development activities for VX-661, a corrector compound discovered under the collaboration, and (ii) additional research and development activities directed at discovering new corrector compounds. Under the April 2011 Amendment, CFFT agreed to provide the Company with up to $75.0 million in funding over approximately five years for corrector-compound research and development activities. The Company retains the right to develop and commercialize KALYDECO (ivacaftor), lumacaftor (VX-809), VX-661 and any other compounds discovered during the course of the research collaboration with CFFT.

During the three and six months ended June 30, 2014 and 2013, the Company recognized the following revenues attributable to the CFFT collaboration:



	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
	(in thousands)
Collaborative revenues attributable to the CFFT collaboration	$	1,604	$	4,244	$	4,472	$	7,803

In the original agreement, as amended prior to the April 2011 Amendment, the Company agreed to pay CFFT tiered royalties calculated as a percentage, ranging from single digits to sub-teens, of annual net sales of any approved drugs discovered during the research term that ended in 2008, including KALYDECO, lumacaftor and VX-661. The April 2011 Amendment provides for a tiered royalty in the same range on net sales of corrector compounds discovered during the research term that began in 2011 and ended in February 2014. In each of the third quarter of 2012 and first quarter of 2013, CFFT earned a commercial milestone payment of $9.3 million from the Company upon achievement of certain sales levels for KALYDECO. These milestones were reflected in the Company's cost of product revenues. There are no additional commercial milestone payments payable by the Company to CFFT related to sales levels for KALYDECO. The Company also is obligated to make up to two one-time commercial milestone payments to CFFT upon achievement of certain sales levels for corrector compounds such as lumacaftor or VX-661.

The Company began marketing KALYDECO in the United States in the first quarter of 2012 and began marketing KALYDECO in certain countries in the European Union in the third quarter of 2012. The Company has royalty obligations to CFFT for each compound commercialized pursuant to this collaboration until the expiration of patents covering that compound. 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 life extensions. CFFT may terminate its funding obligations under the collaboration, as amended, in certain circumstances, in which case there will be a proportional adjustment to the royalty rates and commercial milestone payments for certain corrector compounds. The collaboration also may be terminated by either party for a material breach by the other, subject to notice and cure provisions.

Alios BioPharma, Inc.

License and Collaboration Agreement

In June 2011, the Company entered into a license and collaboration agreement (the “Alios Agreement”) with Alios, a privately-held biotechnology company. Pursuant to the Alios Agreement, the Company and Alios collaborated on the research, development and commercialization of HCV nucleotide analogues discovered by Alios through April 2014. In April 2014, Vertex and Alios amended the Alios Agreement to eliminate the Company's obligations to conduct further development activities with respect to VX-135. The Company does not expect to conduct any further development activities with respect to VX-135 and plans to seek to outlicense its rights to VX-135.

Under the terms of the Alios Agreement, the Company received exclusive worldwide rights to ALS-2200 (now formulated as VX-135) and ALS-2158, a second HCV nucleotide analogue discovered by Alios that was developed pursuant to the Alios agreement through the third quarter of 2012. Alios and the Company began clinical development of ALS-2200 (VX-135) and ALS-2158 in December 2011. The Company is responsible for all costs related to development, commercialization and manufacturing of each compound licensed to the Company pursuant to the Alios Agreement and provided funding to Alios to conduct the Phase 1 clinical trials for ALS-2200 and ALS-2158. In addition, the Company provided funding for a research program, which ended in 2013, directed to the discovery of additional HCV nucleotide analogues that act on the HCV polymerase.

Upon entering into the Alios Agreement, the Company paid Alios a $60.0 million up-front payment. As of June 30, 2014, Alios also had earned an aggregate of $60.0 million in development milestone payments pursuant to the Alios Agreement. The Alios Agreement provides for development milestone payments if VX-135 is approved and commercialized. In addition, Alios is eligible to receive commercial milestone payments, as well as tiered royalties on net sales of VX-135.

The Company may terminate the Alios Agreement upon 60 days’ notice to Alios. The Alios Agreement also may be terminated by either party for a material breach by the other, or if the Company challenges certain Alios patents, in each case subject to notice and cure provisions. Unless earlier terminated, the Alios 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 (a) the date the last-to-expire patent covering a licensed product expires or (b) 10 years after the first commercial sale in the applicable country.

Under applicable accounting guidance, the Company determined that Alios was a VIE, its license to VX-135 and ALS-2158 was a variable interest in Alios, that Alios was a business and that the Company was Alios’ primary beneficiary for the period from June 13, 2011 through December 31, 2013. The Company based these determinations on, among other factors, the significance to Alios of the licensed compounds and on the Company’s power, through the joint steering committee for the licensed compounds established under the Alios Agreement, to direct the activities that most significantly affect the economic performance of Alios.

Accordingly, the Company consolidated Alios’ financial statements with the Company’s condensed consolidated financial statements from June 13, 2011 through December 31, 2013. However, the Company’s interests in Alios were limited to those accorded to the Company in the Alios Agreement. In particular, the Company did not acquire any equity interest in Alios, any interest in Alios’ cash and cash equivalents or any control over Alios’ activities that do not relate to the Alios Agreement. Alios does not have any right to the Company’s assets except as provided in the Alios Agreement.

As of December 31, 2013, the Company determined that it no longer had a variable interest in Alios as a whole and did not possess the power to direct the activities that most significantly affect the economic performance of Alios based on, among other factors, the decline in significance to Alios of the licensed HCV nucleotide analogue program. The Company deconsolidated Alios based on this conclusion as of December 31, 2013.

The Company continues to have significant continuing involvement with Alios due to the Alios Agreement, as amended; therefore, the deconsolidation of Alios is not presented as discontinued operations in the Company's condensed consolidated financial statements as of June 30, 2014. The Company will evaluate whether it continues to have significant continuing involvement with Alios for a period of one year from the December 31, 2013 deconsolidation date.

Noncontrolling Interest (Alios)

Prior to the deconsolidation, the Company recorded net loss (income) attributable to noncontrolling interest (Alios) on its condensed consolidated statements of operations, reflecting Alios' net loss (income) for the reporting period, adjusted for changes in the fair value of contingent milestone payments and royalties payable by the Company to Alios, which was evaluated each reporting period. A summary of net loss attributable to noncontrolling interest (Alios) for the three and six months ended June 30, 2013 is as follows:



	Three Months Ended June 30, 2013			Six Months Ended June 30, 2013
	(in thousands)
Loss before benefit from income taxes	$	6,824		$	12,121
Decrease in fair value of contingent milestone and royalty payments	80			2,820
Benefit from income taxes	(2,357		)	(5,783		)
Net loss attributable to noncontrolling interest (Alios)	$	4,547		$	9,158

The Company did not have a corresponding net loss (income) attributable to noncontrolling interest (Alios) for the three and six months ended June 30, 2014 due to the deconsolidation of Alios.

The Company used present-value models to determine the estimated fair value of the contingent milestone and royalty payments until it deconsolidated Alios, based on assumptions regarding the probability of achieving the relevant milestones, estimates regarding the time to develop drug candidates, estimates of future product sales and the appropriate discount and tax rates. The Company based 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 represented a measure of credit risk associated with settling the liability. Significant judgment was used in determining the appropriateness of these assumptions at each reporting period.

Janssen Pharmaceuticals, Inc.

On June 11, 2014, the Company entered into a license, development and commercialization agreement (the "Janssen Inc. Agreement") with Janssen Pharmaceuticals, Inc. (“Janssen Inc.”) pursuant to which it granted Janssen Inc. an exclusive worldwide license to develop and commercialize VX-787 and a backup compound referred to as VX-353, for the treatment of influenza. In connection with the execution of the Janssen Inc. Agreement, the Company received from Janssen Inc. an up-front payment of $30.0 million in the third quarter of 2014. In addition, Vertex has the potential to receive development and commercial milestone payments as well as royalties on any future product sales.

Janssen Inc. will be responsible for costs related to the development and commercialization of the compounds. Janssen Inc. may terminate the Janssen Inc. Agreement, subject to certain exceptions, upon six months' notice. The Janssen Inc. 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 Janssen Inc. Agreement will continue in effect until the expiration of Janssen Inc.'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 applicable country.

The Company will evaluate the deliverables pursuant to the Janssen Inc. Agreement under multiple element arrangement guidance for collaborative arrangements during the third quarter of 2014. The collaboration with Janssen Inc. was subject to the expiration of the waiting period under the Hart–Scott–Rodino Antitrust Improvements Act of 1976. The waiting period expired in July 2014; therefore, there was no accounting impact for the three and six months ended June 30, 2014.

Net Loss Per Share Attributable to Vertex Common Shareholders

6 Months Ended

Jun. 30, 2014

Earnings Per Share [Abstract]

Net Loss Per Share Attributable to Vertex Common Stockholders

Net Loss Per Share Attributable to Vertex Common Shareholders

Basic net loss attributable to Vertex per common share 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 described in the following table in the computation of the net loss attributable to Vertex per common share calculations because the effect would have been anti-dilutive during each period:



	Three Months Ended June 30,		Six Months Ended June 30,
	2014	2013	2014	2013
	(in thousands)
Stock options	14,549	16,802	14,549	16,802
Unvested restricted stock and restricted stock units	2,584	2,600	2,584	2,600

Fair Value Measurements

6 Months Ended

Jun. 30, 2014

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 June 30, 2014, the Company’s investments were in money market funds, government-sponsored enterprise securities, corporate debt securities and commercial paper.

As of June 30, 2014, 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 government-sponsored enterprise securities. The Company’s financial assets valued based on Level 2 inputs consisted of corporate debt securities and commercial paper, which consist of investments in highly-rated investment-grade corporations. During the three and six months ended June 30, 2014 and 2013, the Company did not record an other-than-temporary impairment charge related to its financial assets.

The following table sets forth the Company’s financial assets subject to fair value measurements:



	Fair Value Measurements as of June 30, 2014
			Fair Value Hierarchy
	Total		Level 1		Level 2		Level 3
	(in thousands)
Financial assets carried at fair value:
Cash equivalents:
Money market funds	$	123,469	$	123,469	$	—	$	—
Marketable securities:
Government-sponsored enterprise securities	497,587		497,587		—		—
Commercial paper	69,243		—		69,243		—
Corporate debt securities	231,773		—		231,773		—
Total	$	922,072	$	621,056	$	301,016	$	—

The fair value of the Company’s foreign currency forward contracts, which were not material as of June 30, 2014, were based on Level 2 inputs. The fair value of the outstanding foreign currency forward contract were determined using third party pricing services. Please refer to Note H, "Hedging," for further information regarding the Company’s foreign currency forward contracts.

- 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

6 Months Ended

Jun. 30, 2014

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 June 30, 2014
Cash and cash equivalents:
Cash and money market funds	$	420,558	$	—	$	—		$	420,558
Total cash and cash equivalents	$	420,558	$	—	$	—		$	420,558
Marketable securities:
Government-sponsored enterprise securities (due within 1 year)	$	497,601	$	8	$	(22	)	$	497,587
Commercial paper (due within 1 year)	69,144		99		—			69,243
Corporate debt securities (due within 1 year)	216,426		33		(26		)	216,433
Corporate debt securities (due after 1 year through 5 years)	15,335		5		—			15,340
Total marketable securities	$	798,506	$	145	$	(48	)	$	798,603
Total cash, cash equivalents and marketable securities	$	1,219,064	$	145	$	(48	)	$	1,219,161

As of December 31, 2013
Cash and cash equivalents:
Cash and money market funds	$	569,299	$	—	$	—		$	569,299
Total cash and cash equivalents	$	569,299	$	—	$	—		$	569,299
Marketable securities:
Government-sponsored enterprise securities (due within 1 year)	$	600,496	$	7	$	(53	)	$	600,450
Commercial paper (due within 1 year)	83,384		109		—			83,493
Corporate debt securities (due within 1 year)	189,674		14		(34		)	189,654
Corporate debt securities (due after 1 year through 5 years)	22,181		6		(7		)	22,180
Total marketable securities	$	895,735	$	136	$	(94	)	$	895,777
Total cash, cash equivalents and marketable securities	$	1,465,034	$	136	$	(94	)	$	1,465,076

Accumulated Other Comprehensive Loss

6 Months Ended

Jun. 30, 2014

Equity [Abstract]

Accumulated Other Comprehensive Loss

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



	Foreign Currency Translation Adjustment			Unrealized Holding Gains on Marketable Securities		Unrealized Losses on Foreign Currency Forward Contracts			Total
	(in thousands)
Balance at December 31, 2013	$	(325	)	$	42	$	(23	)	$	(306	)
Other comprehensive income (loss) before reclassifications	353			55		(108		)	300
Amounts reclassified from accumulated other comprehensive loss	—			—		(17		)	(17		)
Net current period other comprehensive income (loss)	$	353		$	55	$	(125	)	$	283
Balance at June 30, 2014	$	28		$	97	$	(148	)	$	(23	)



	Foreign Currency Translation Adjustment			Unrealized Holding Gains (Losses) on Marketable Securities			Unrealized Gains (Losses) on Foreign Currency Forward Contracts		Total
	(in thousands)
Balance at December 31, 2012	$	(746	)	$	196		$	—	$	(550	)
Other comprehensive loss before reclassifications	(521		)	(159		)	—		(680		)
Amounts reclassified from accumulated other comprehensive loss	—			—			—		—
Net current period other comprehensive loss	$	(521	)	$	(159	)	$	—	$	(680	)
Balance at June 30, 2013	$	(1,267	)	$	37		$	—	$	(1,230	)

- 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=36458714&loc=d3e689-108580

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=36458714&loc=SL7669619-108580

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 12
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e640-108580

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 17
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e716-108580

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 16
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e709-108580

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e637-108580

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 14
-URI http://asc.fasb.org/extlink&oid=36458714&loc=d3e681-108580

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Reclassification Adjustments
-URI http://asc.fasb.org/extlink&oid=6522872

+ Details

Hedging

6 Months Ended

Jun. 30, 2014

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Hedging

In December 2013, the Company initiated 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 included foreign currency forward contracts that were designated as cash flow hedges under GAAP having remaining contractual durations from one to twelve 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 (i) a foreign currency forward contract is not highly effective as a cash flow hedge, (ii) it has ceased to be a highly effective hedge or (iii) a 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 June 30, 2014, all hedges were determined to be highly effective.

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



	As of June 30, 2014		As of December 31, 2013
Foreign Currency	(in thousands)
Euro	$	23,334	$	17,468
British pound sterling	16,921		—
Total foreign currency forward contracts	$	40,255	$	17,468

Changes in fair value of these foreign currency forward contracts are included in accumulated other comprehensive loss as unrealized gains and losses until the forecasted underlying transaction occurs. Unrealized gains and losses on these foreign currency forward contracts are included in (i) prepaid expenses and other current assets and (ii) other liabilities, current portion, respectively, on the Company's condensed consolidated balance sheets. Realized gains and losses for the effective portion of such contracts are recognized in product revenues, net in the condensed consolidated statement of operations when the contract is settled with the counterparty. Cash flows from foreign currency forward contracts are classified within cash flows from operating activities in the same category as the cash flows from the hedged item.

The following table summarizes the fair value of the Company's outstanding foreign currency forward contracts included on the Company's condensed consolidated balance sheets:



	As of June 30, 2014			As of December 31, 2013
	(in thousands)
Fair value - assets	$	50		$	—
Fair value - liabilities	(198		)	(23		)
Net carrying value	$	(148	)	$	(23	)

- 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.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 30
-Section 45
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6441202&loc=d3e80720-113993

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4C
-URI http://asc.fasb.org/extlink&oid=35706170&loc=SL5624171-113959

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=35706170&loc=d3e41620-113959

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4B
-URI http://asc.fasb.org/extlink&oid=35706170&loc=SL5624163-113959

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=35706170&loc=SL5579240-113959

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4D
-URI http://asc.fasb.org/extlink&oid=35706170&loc=SL5624177-113959

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 30
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=35736893&loc=d3e80784-113994

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=35706170&loc=d3e41641-113959

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=35706170&loc=SL5579245-113959

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4H
-URI http://asc.fasb.org/extlink&oid=35706170&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=35706170&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=35706170&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=35706170&loc=SL5618551-113959

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 1B
-URI http://asc.fasb.org/extlink&oid=35706170&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=35706170&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=35706170&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

6 Months Ended

Jun. 30, 2014

Inventory Disclosure [Abstract]

Inventories

The following table sets forth the Company’s inventories by type:



	As of June 30, 2014		As of December 31, 2013
	(in thousands)
Raw materials	$	—	$	489
Work-in-process	11,013		9,981
Finished goods	969		3,677
Total	$	11,982	$	14,147

Intangible Assets and Goodwill	6 Months Ended
Intangible Assets and Goodwill	Jun. 30, 2014
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible Assets and Goodwill	Intangible Assets and Goodwill Intangible Assets As of June 30, 2014, the Company had no intangible assets recorded on its condensed consolidated balance sheet. The intangible assets that were previously reflected on the Company's condensed consolidated balance sheets related to drug candidates for the treatment of HCV infection. The field of HCV infection treatment is highly competitive and characterized by rapid technological advances and the development of drug candidates for the treatment of HCV infection is subject to numerous risks. Two of the Company's competitors received approval in the fourth quarter of 2013 for new treatment regimens for HCV infection that include pegylated-interferon and ribavirin, and several of the Company's competitors are conducting Phase 3 clinical trials evaluating all-oral combinations of their drug candidates for the treatment of HCV infection. ViroChem Acquisition The Company determined that the fair value of the VX-222 intangible asset of $412.9 million acquired from ViroChem was zero as of March 31, 2013. Accordingly, the Company recorded a $412.9 million impairment charge in the three months ended March 31, 2013 and the six months ended June 30, 2013. In connection with this impairment charge, the Company recorded a credit of $127.6 million in its provision for income taxes. In the six months ended June 30, 2013, the increase to the Company's net loss attributable to Vertex related to this impairment charge, net of the tax credit, was $285.3 million, and the net increase to the Company's net loss per share attributable to Vertex common shareholders was $1.30 per share. Alios Collaboration In June 2011, the Company recorded $250.6 million of intangible assets on its condensed consolidated balance sheet based on the Company's estimate of the fair value of Alios' HCV nucleotide analogue program, including the intellectual property related to ALS-2200 and ALS-2158. In the fourth quarter of 2013, the Company determined that the fair value of the HCV nucleotide analogue program was zero as of December 31, 2013. Accordingly, in the fourth quarter of 2013, the Company recorded a $250.6 million impairment charge and a $102.1 million benefit from income taxes. Goodwill As of June 30, 2014 and December 31, 2013, goodwill of $31.0 million was recorded on the Company's condensed consolidated balance sheets. There was no change to goodwill recorded during the three and six months ended June 30, 2014 or 2013.

- 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

Convertible Senior Subordinated Notes	6 Months Ended
Convertible Senior Subordinated Notes	Jun. 30, 2014
Debt Disclosure [Abstract]
Convertible Senior Subordinated Notes	Convertible Senior Subordinated Notes In 2010, the Company completed an offering of $400.0 million in aggregate principal amount of 3.35% convertible senior subordinated notes due 2015 (the "2015 Notes"). This offering resulted in $391.6 million of net proceeds to the Company. The underwriting discount and other expenses of $8.4 million were recorded as debt issuance costs and were included in other assets on the Company’s condensed consolidated balance sheets. The 2015 Notes were convertible at any time, at the option of the holder, into common stock at a price equal to approximately $48.83 per share, or 20.4794 shares of common stock per $1,000 principal amount of the 2015 Notes. If the closing price of the Company’s common stock exceeded 130% of the conversion price for at least 20 trading days within a period of 30 consecutive trading days, the Company had the right to redeem the 2015 Notes at its option at a redemption price equal to 100% of the principal amount of the 2015 Notes to be redeemed. In the second quarter of 2013, the Company's common stock exceeded 130% of the conversion price of the 2015 Notes for at least 20 trading days within a period of 30 consecutive trading days, and the Company notified the holders of the 2015 Notes that it would redeem the 2015 Notes on June 17, 2013. In response to the Company's call of the 2015 Notes for redemption, in accordance with the provisions of the 2015 Notes, the holders of $399.8 million in aggregate principal amount of 2015 Notes elected to convert their 2015 Notes into the Company's common stock at the conversion price of approximately $48.83 per share. As a result of these conversions, the Company issued 8,188,448 shares of common stock. The remaining $0.2 million in aggregate principal amount of 2015 Notes was redeemed on June 17, 2013. Pursuant to the terms of the 2015 Notes, the Company made an additional payment of $16.75 per $1,000 principal amount, payable in shares of the Company’s common stock, to the holders of the 2015 Notes that converted or redeemed their 2015 Notes after the Company called the 2015 Notes for redemption. These payments resulted in the issuance of an additional 87,109 shares of the Company's common stock. In the second quarter of 2013, the Company recognized an aggregate of $6.7 million in interest expense related to the 2015 Notes. Unamortized debt issuance costs for the 2015 Notes of $4.2 million were recorded as an offset to additional paid-in capital.

Long-term Obligations

6 Months Ended

Jun. 30, 2014

Long-term Debt and Capital Lease Obligations [Abstract]

Long-term Obligations

Fan Pier Leases

In 2011, the Company entered into two leases, 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, including having responsibility to pay for a portion of the costs of finish work and structural elements of the Buildings, the Company was deemed for accounting purposes to be the owner of the Buildings during the construction period. Therefore, the Company recorded project construction costs incurred by the landlord as an asset and a related financing obligation during the construction period. The Company evaluated the Fan Pier Leases in the fourth quarter of 2013 and determined that the Fan Pier Leases did not meet the criteria for “sale-leaseback” treatment. This determination was based on, among other things, the Company's continuing involvement with the property in the form of non-recourse financing to the lessor. Accordingly, the Company began depreciating the asset and incurring interest expense related to the financing obligation during the fourth quarter of 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 $522.2 million and $503.4 million as of June 30, 2014 and December 31, 2013, respectively, related to construction costs for the Buildings at Fan Pier in Boston, Massachusetts. The construction financing lease obligation related to the Buildings at Fan Pier was $473.6 million and $440.9 million as of June 30, 2014 and December 31, 2013, respectively.

Capital Leases

The Company has outstanding capital leases for equipment, leasehold improvements and software licenses with terms through 2019. The following table sets forth the Company’s future minimum payments due under capital leases as of June 30, 2014:



Year	(in thousands)
2014	$	9,519
2015	20,792
2016	14,254
2017	13,129
2018	13,027
2019	3,047
Thereafter	—
Total payments	$	73,768
Less: amount representing interest	(9,008		)
Present value of payments	$	64,760

Financing Arrangements

The Company has outstanding $33.5 million in irrevocable stand-by letters of credit issued in connection with property leases and other similar agreements that currently are supported by an unsecured credit facility that expires in September 2014.

Stock-based Compensation Expense

6 Months Ended

Jun. 30, 2014

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

Stock-based Compensation Expense

The Company issues stock options, restricted stock and restricted stock units with service conditions, which are generally the vesting periods of the awards. The Company also has issued, to certain members of senior management, restricted stock and restricted stock units that vest upon the earlier of the satisfaction of (i) a performance condition or (ii) a service condition, and stock options that vest upon the earlier of the satisfaction of (a) performance conditions or (b) a service condition. In addition, the Company issues shares pursuant to an employee stock purchase plan ("ESPP").

Effective for equity awards granted on or after February 5, 2014, the Company provides to employees who have rendered significant service to the Company and meet certain age requirements, partial or full acceleration of vesting of certain equity awards upon a termination of employment other than for cause. Less than 5% of the Company’s employees were eligible for partial or full acceleration of their equity awards as of June 30, 2014. The Company recognizes stock-based compensation expense related to these awards over the service period from the date of grant until the qualified employees become eligible for partial or full acceleration of vesting.

During the three and six months ended June 30, 2014 and 2013, the Company recognized the following stock-based compensation expense:



	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
	(in thousands)
Stock-based compensation expense by type of award:
Stock options	$	26,985		$	29,949		$	52,112		$	49,623
Restricted stock and restricted stock units	14,020			9,732			33,013			19,110
ESPP share issuances	1,681			2,051			4,348			4,573
Less stock-based compensation expense capitalized to inventories	(242		)	(382		)	(449		)	(681		)
Total stock-based compensation expense included in costs and expenses	$	42,444		$	41,350		$	89,024		$	72,625

Stock-based compensation expense by line item:
Research and development expenses	$	27,253		$	25,740		$	60,153		$	45,089
Sales, general and administrative expenses	15,191			15,610			28,871			27,536
Total stock-based compensation expense included in costs and expenses	$	42,444		$	41,350		$	89,024		$	72,625

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 June 30, 2014
	Unrecognized Expense, Net of Estimated Forfeitures		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Stock options	$	158,362	2.33
Restricted stock and restricted stock units	$	102,006	2.14
ESPP share issuances	$	4,082	0.58

The following table summarizes information about stock options outstanding and exercisable at June 30, 2014:



	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)
$10.41–$20.00	368	2.01	$15.59	368	$15.59
$20.01–$30.00	889	5.42	$29.46	708	$29.35
$30.01–$40.00	4,876	5.17	$36.20	3,758	$35.73
$40.01–$50.00	3,508	8.37	$46.32	890	$46.55
$50.01–$60.00	1,348	7.34	$54.11	800	$54.63
$60.01–$70.00	129	9.15	$65.71	20	$64.33
$70.01–$80.00	2,095	9.60	$76.73	308	$74.18
$80.01–$88.18	1,336	9.02	$83.11	375	$82.53
Total	14,549	7.10	$49.77	7,227	$41.65

Sale of HIV Protease Inhibitor Royalty Stream	6 Months Ended
Sale of HIV Protease Inhibitor Royalty Stream	Jun. 30, 2014
Sale of HIV Protease Inhibitor Royalty Stream
Sale of HIV Protease Inhibitor Royalty Stream	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 June 30, 2014, the Company had $53.9 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	6 Months Ended
Income Taxes	Jun. 30, 2014
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company is subject to U.S. federal, state, and foreign income taxes. For the three and six months ended June 30, 2014, the Company recorded a net provision for income taxes of $0.7 million and $1.5 million, respectively, related to state income taxes and income earned in various foreign jurisdictions. For the three and six months ended June 30, 2013, the Company recorded a benefit from income taxes of $1.8 million and $132.1 million, respectively. The benefit from income taxes in the six months ended June 30, 2013 primarily related to a tax benefit associated with the Company’s impairment of VX-222 in the first quarter of 2013. Please refer to "Note J, "Intangible Assets and Goodwill," for further information regarding the impairment charge. As of June 30, 2014 and December 31, 2013, the Company had unrecognized tax benefits of $3.0 million and $2.0 million, respectively. The Company recognizes interest and penalties related to income taxes as a component of income tax expense. As of June 30, 2014, 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 June 30, 2014 and December 31, 2013. 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 U.S. 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 2010 and any other major taxing jurisdiction for years before 2007, except where the Company has net operating losses or tax credit carryforwards that originated before 2005. The Company concluded an audit by Revenue Quebec for the year ended December 31, 2011 with no material changes. The Company is currently under examination by Revenue Quebec for the year ended December 31, 2012 as well as the Massachusetts Department of Revenue and the Internal Revenue Service for the year ended December 31, 2011. No adjustments have been reported. The Company is not under examination by any other jurisdictions for any tax year. The Company currently intends to reinvest the total amount of its unremitted earnings, which have not been significant to date, in the local international jurisdiction or to repatriate the earnings only when tax-effective. As a result, the Company has not provided for U.S. federal income taxes on the unremitted earnings of its international subsidiaries. Upon repatriation of those earnings, in the form of dividends or otherwise, the Company would be subject to U.S. federal income taxes (subject to an adjustment for foreign tax credits) and withholding taxes payable to the various foreign countries. At June 30, 2014, 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.

Restructuring Liabilities

6 Months Ended

Jun. 30, 2014

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 six months ended June 30, 2014 and 2013 were as follows:



	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
	(in thousands)
Liability, beginning of the period	$	18,324		$	22,459		$	19,115		$	23,328
Cash payments	(3,960		)	(3,849		)	(7,822		)	(7,422		)
Cash received from subleases	2,689			2,666			5,378			5,331
Restructuring (income) expense	(2,117		)	776			(1,735		)	815
Liability, end of the period	$	14,936		$	22,052		$	14,936		$	22,052

Fan Pier Move Restructuring

In connection with the relocation of its Massachusetts operations to Fan Pier in Boston, Massachusetts, the Company is incurring restructuring charges related to its remaining lease obligations at its facilities in Cambridge, Massachusetts, which will include lease obligations related to the 120,000 square feet of the Kendall Square facility that the Company continued to use for its operations following its 2003 Kendall Restructuring. The Company started incurring these charges in the fourth quarter of 2013 and expects them to continue through April 2018. The majority of these restructuring charges relate to cease use charges that the Company expects to incur in the third quarter of 2014 once it has vacated the buildings in Cambridge in their entirety. Once the Company completes the relocation, the continuing charges will relate to the difference between the Company’s estimated future cash flows related to its lease obligations and its actual cash flows.

The activities related to the restructuring liability for the three and six months ended June 30, 2014 were as follows:



	Three Months Ended June 30, 2014			Six Months Ended June 30, 2014
	(in thousands)
Liability, beginning of the period	$	3,722		$	797
Cash payments	(2,143		)	(4,377		)
Restructuring expense	1,677			6,836
Liability, end of the period	$	3,256		$	3,256

Strategic Restructuring

In October 2013, the Company adopted a restructuring plan. The restructuring plan 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 cystic fibrosis and other research and development programs.

The activities related to the restructuring liability for the three and six months ended June 30, 2014 were as follows:



	Three Months Ended June 30, 2014			Six Months Ended June 30, 2014
	(in thousands)
Liability, beginning of the period	$	1,821		$	8,441
Cash payments	(1,199		)	(8,466		)
Restructuring expense	170			817
Liability, end of the period	$	792		$	792

Other Income (Expense), Net	6 Months Ended
Other Income (Expense), Net	Jun. 30, 2014
Other Income and Expenses [Abstract]
Other Income (Expense), Net	Other Income (Expense), Net In April 2014, the Company received a one-time cash payment of $36.7 million from its landlord pursuant to the Fan Pier Leases. This payment related to bonds issued pursuant to an Infrastructure Development Assistance Agreement between The Commonwealth of Massachusetts and the Company’s landlord. The bonds were issued in connection with the landlord’s contribution to infrastructure improvements and also were dependent upon employment levels at the Company through the bond issuance date. The Company accounted for the cash payment as a government grant as it was provided in part related to the Company's employment level in Massachusetts. Such grants are recognized in income in the period in which the conditions of the grant are met and there is reasonable assurance that the grant will be received, provided it is not subject to refund. In the second quarter of 2014, the Company recorded $36.7 million as a credit to other income (expense), net in its condensed consolidated statements of operations for the three and six months ended June 30, 2014 because the Company's employment obligations related to these funds were satisfied as of the date of issuance of the bonds and the payment received is not subject to refund.

Legal Proceedings	6 Months Ended
Legal Proceedings	Jun. 30, 2014
Legal Proceedings [Abstract]
Legal Proceedings	Legal Proceedings City of Bristol Pension Fund v. Vertex Pharmaceuticals Incorporated, et al. On September 6, 2012, a purported shareholder class action, City of Bristol Pension Fund 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 June 28, 2012, all in violation of Section 10(b) of the Securities Exchange Act of 1934, as amended, and Rule 10b-5 promulgated thereunder. By order dated December 12, 2012, the court appointed the City of Bristol lead plaintiff and appointed the City of Bristol's attorneys lead counsel. The plaintiffs filed an amended complaint on February 11, 2013. The Company filed a motion to dismiss the complaint on April 12, 2013. On May 28, 2013, the plaintiffs filed an opposition to the Company's motion to dismiss the complaint. On June 27, 2013, the Company filed a reply in further support of the Company's motion to dismiss the plaintiffs' complaint. The court conducted a hearing on the Company's motion to dismiss on November 25, 2013, and the court dismissed the plaintiffs' complaint on March 31, 2014. The plaintiffs filed a motion (i) for reconsideration and (ii) to file a second amended complaint on April 28, 2014. On May 23, 2014, the court denied the plaintiffs' motion and dismissed the complaint with prejudice. Local No. 8 IBEW Retirement Plan & Trust v. Vertex Pharmaceuticals Incorporated, et al. 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. The Company believes the claims to be without merit and intends to vigorously defend the litigation. As of June 30, 2014, the Company has not recorded any reserves for this purported class action.

Contingencies	6 Months Ended
Contingencies	Jun. 30, 2014
Commitments and Contingencies Disclosure [Abstract]
Contingencies	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 June 30, 2014 or December 31, 2013.

- Definition

The entire disclosure for loss and gain contingencies. Describes any existing condition, situation, or set of circumstances involving uncertainty as of the balance sheet date (or prior to issuance of the financial statements) as to a probable or reasonably possible loss incurred by an entity that will ultimately be resolved when one or more future events occur or fail to occur, and typically discloses the amount of loss recorded or a range of possible loss, or an assertion that no reasonable estimate can be made.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=25496072&loc=d3e14472-108349

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 460
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6851643&loc=d3e12021-110248

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=25496072&loc=d3e14326-108349

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=25496072&loc=d3e14394-108349

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 9
-URI http://asc.fasb.org/extlink&oid=25496072&loc=d3e14557-108349

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 460
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6851643&loc=d3e12053-110248

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=25496072&loc=d3e14435-108349

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=25496072&loc=d3e14453-108349

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=25496072&loc=d3e14615-108349

+ Details

Guarantees	6 Months Ended
Guarantees	Jun. 30, 2014
Guarantees [Abstract]
Guarantees	Guarantees 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.

Subsequent Events	6 Months Ended
Subsequent Events	Jun. 30, 2014
Debt Disclosure [Abstract]
Subsequent Events	On July 9, 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 provides for a $300.0 million senior secured term loan. The credit agreement also provides that, subject to satisfaction of certain conditions, the Company may request that the lenders establish an incremental senior secured term loan facility in an aggregate amount not to exceed $200.0 million. The loan initially bears interest at a rate of 7.2% per annum but shall be reduced to 6.2% per annum on the later to occur of (i) FDA approval in the United States of a product with a label claim for treating patients with cystic fibrosis 12 years of age and older who are homozygous with the F508del mutation, or FDA Approval, and (ii) the one year anniversary of the closing, in each case, until the second anniversary of the closing. On and after the second anniversary of the closing, the loan will bear interest at a rate per annum equal to LIBOR plus 5.0% to 7.5% depending on the receipt of FDA Approval. The maturity date of all loans under the facilities is July 9, 2017. Interest is payable quarterly and on the maturity date. The Company is required to repay principal on the loan in installments of $15.0 million per quarter from October 1, 2015 through July 1, 2016 and in installments of $60.0 million per quarter from October 1, 2016 through the maturity date. The Company may prepay the loans, in whole or in part, at any time; provided that prepayments prior to the second anniversary of the closing are subject to a make-whole premium. The Company's obligations under the facilities are unconditionally guaranteed by certain of its domestic subsidiaries. All obligations under the facilities, and the guarantees of those obligations, are secured, subject to certain exceptions, by substantially all of the Company's assets and the assets of all guarantors, including the pledge of all or a portion of the equity interests of certain of its subsidiaries. The credit agreement requires that the Company maintain, on a quarterly basis, a minimum level of KALYDECO net revenues. Further, the credit agreement includes negative covenants, subject to exceptions, restricting or limiting the Company's ability and the ability of its subsidiaries to, among other things, incur additional indebtedness, grant liens, engage in certain investment, acquisition and disposition transactions, pay dividends, repurchase capital stock and enter into transactions with affiliates. The credit agreement also contains customary representations and warranties, affirmative covenants and events of default, including payment defaults, breach of representations and warranties, covenant defaults and cross defaults. If an event of default occurs, the administrative agent would be entitled to take various actions, including the acceleration of amounts due under outstanding loans.

Basis of Presentation and Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 2014
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 and (ii) its wholly-owned subsidiaries. In addition, the condensed consolidated financial statements for the period from June 13, 2011 through December 31, 2013, reflect the operations of Alios BioPharma, Inc. (“Alios”), a collaborator that was a variable interest entity (a “VIE”) for which the Company was deemed under applicable accounting guidance to have a variable interest and be the primary beneficiary. As of December 31, 2013, the Company deconsolidated Alios, and the Company's consolidated balance sheets as of June 30, 2014 and December 31, 2013 exclude Alios. 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 June 30, 2014 and 2013. 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, 2013, which are contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2013 that was filed with the Securities and Exchange Commission (the “SEC”) on February 11, 2014 (the "2013 Annual Report on Form 10-K").
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, noncontrolling interest (Alios), the consolidation and deconsolidation of a VIE, leases and the income tax provision. 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 2013 Annual Report on Form 10-K.
Recent Accounting Pronouncements	Recent Accounting Pronouncements For a discussion of recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2013 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the six months ended June 30, 2014 that had a material effect on the Company's condensed consolidated financial statements. In the second quarter of 2014, the Financial Accounting Standards Board issued amended guidance applicable to revenue recognition that will be effective for the Company for the year ending December 31, 2017. The new guidance must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach. Early adoption is not permitted. The new guidance applies a more principles-based approach to recognizing revenue. The Company is evaluating the new guidance and the expected effect on the Company’s condensed consolidated financial statements.

Product Revenues, Net (Tables)

6 Months Ended

Jun. 30, 2014

Product Revenues [Abstract]

Schedule of product revenues and allowances and reserve categories

The following table summarizes activity in each of the product revenue allowance and reserve categories for the six months ended June 30, 2014:



	Trade Allowances			Rebates, Chargebacks and Discounts			Product Returns			Other Incentives			Total
	(in thousands)
Balance at December 31, 2013	$	1,535		$	68,244		$	15,799		$	1,555		$	87,133
Provision related to current period sales	4,513			26,464			379			859			32,215
Adjustments related to prior period sales	(8		)	3,861			4,124			1			7,978
Credits/payments made	(5,271		)	(57,617		)	(4,160		)	(1,586		)	(68,634		)
Balance at June 30, 2014	$	769		$	40,952		$	16,142		$	829		$	58,692

Collaborative Arrangements (Tables)

6 Months Ended

Jun. 30, 2014

Collaborative Arrangements

Collaborator revenues

During the three and six months ended June 30, 2014 and 2013, the Company recognized the following revenues attributable to the CFFT collaboration:



	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
	(in thousands)
Collaborative revenues attributable to the CFFT collaboration	$	1,604	$	4,244	$	4,472	$	7,803

During the three and six months ended June 30, 2014 and 2013, the Company recognized the following revenues attributable to the Janssen NV collaboration:



	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
	(in thousands)
Royalty revenues (INCIVO)	$	5,698	$	44,070	$	10,633	$	83,114
Collaborative revenues:
Up-front and amendment payments revenues	$	—	$	3,107	$	—	$	6,214
Net reimbursement for telaprevir development costs	1,483		37		2,872		9
Reimbursement for manufacturing services	—		—		—		10,299
Total collaborative revenues attributable to the Janssen NV collaboration	$	1,483	$	3,144	$	2,872	$	16,522
Total revenues attributable to the Janssen NV collaboration	$	7,181	$	47,214	$	13,505	$	99,636

Summary of activity related to net loss (income) attributable to noncontrolling interest (Alios)

A summary of net loss attributable to noncontrolling interest (Alios) for the three and six months ended June 30, 2013 is as follows:



	Three Months Ended June 30, 2013			Six Months Ended June 30, 2013
	(in thousands)
Loss before benefit from income taxes	$	6,824		$	12,121
Decrease in fair value of contingent milestone and royalty payments	80			2,820
Benefit from income taxes	(2,357		)	(5,783		)
Net loss attributable to noncontrolling interest (Alios)	$	4,547		$	9,158

Net Loss Per Share Attributable to Vertex Common Shareholders (Tables)

6 Months Ended

Jun. 30, 2014

Earnings Per Share [Abstract]

Potential gross common equivalent shares



	Three Months Ended June 30,		Six Months Ended June 30,
	2014	2013	2014	2013
	(in thousands)
Stock options	14,549	16,802	14,549	16,802
Unvested restricted stock and restricted stock units	2,584	2,600	2,584	2,600

Fair Value Measurements (Tables)

6 Months Ended

Jun. 30, 2014

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 subject to fair value measurements:



	Fair Value Measurements as of June 30, 2014
			Fair Value Hierarchy
	Total		Level 1		Level 2		Level 3
	(in thousands)
Financial assets carried at fair value:
Cash equivalents:
Money market funds	$	123,469	$	123,469	$	—	$	—
Marketable securities:
Government-sponsored enterprise securities	497,587		497,587		—		—
Commercial paper	69,243		—		69,243		—
Corporate debt securities	231,773		—		231,773		—
Total	$	922,072	$	621,056	$	301,016	$	—

Marketable Securities (Tables)

6 Months Ended

Jun. 30, 2014

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 June 30, 2014
Cash and cash equivalents:
Cash and money market funds	$	420,558	$	—	$	—		$	420,558
Total cash and cash equivalents	$	420,558	$	—	$	—		$	420,558
Marketable securities:
Government-sponsored enterprise securities (due within 1 year)	$	497,601	$	8	$	(22	)	$	497,587
Commercial paper (due within 1 year)	69,144		99		—			69,243
Corporate debt securities (due within 1 year)	216,426		33		(26		)	216,433
Corporate debt securities (due after 1 year through 5 years)	15,335		5		—			15,340
Total marketable securities	$	798,506	$	145	$	(48	)	$	798,603
Total cash, cash equivalents and marketable securities	$	1,219,064	$	145	$	(48	)	$	1,219,161

As of December 31, 2013
Cash and cash equivalents:
Cash and money market funds	$	569,299	$	—	$	—		$	569,299
Total cash and cash equivalents	$	569,299	$	—	$	—		$	569,299
Marketable securities:
Government-sponsored enterprise securities (due within 1 year)	$	600,496	$	7	$	(53	)	$	600,450
Commercial paper (due within 1 year)	83,384		109		—			83,493
Corporate debt securities (due within 1 year)	189,674		14		(34		)	189,654
Corporate debt securities (due after 1 year through 5 years)	22,181		6		(7		)	22,180
Total marketable securities	$	895,735	$	136	$	(94	)	$	895,777
Total cash, cash equivalents and marketable securities	$	1,465,034	$	136	$	(94	)	$	1,465,076

Accumulated Other Comprehensive Loss (Tables)

6 Months Ended

Jun. 30, 2014

Equity [Abstract]

Accumulated Other Comprehensive Loss

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



	Foreign Currency Translation Adjustment			Unrealized Holding Gains on Marketable Securities		Unrealized Losses on Foreign Currency Forward Contracts			Total
	(in thousands)
Balance at December 31, 2013	$	(325	)	$	42	$	(23	)	$	(306	)
Other comprehensive income (loss) before reclassifications	353			55		(108		)	300
Amounts reclassified from accumulated other comprehensive loss	—			—		(17		)	(17		)
Net current period other comprehensive income (loss)	$	353		$	55	$	(125	)	$	283
Balance at June 30, 2014	$	28		$	97	$	(148	)	$	(23	)



	Foreign Currency Translation Adjustment			Unrealized Holding Gains (Losses) on Marketable Securities			Unrealized Gains (Losses) on Foreign Currency Forward Contracts		Total
	(in thousands)
Balance at December 31, 2012	$	(746	)	$	196		$	—	$	(550	)
Other comprehensive loss before reclassifications	(521		)	(159		)	—		(680		)
Amounts reclassified from accumulated other comprehensive loss	—			—			—		—
Net current period other comprehensive loss	$	(521	)	$	(159	)	$	—	$	(680	)
Balance at June 30, 2013	$	(1,267	)	$	37		$	—	$	(1,230	)

Hedging (Tables)

6 Months Ended

Jun. 30, 2014

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 June 30, 2014		As of December 31, 2013
Foreign Currency	(in thousands)
Euro	$	23,334	$	17,468
British pound sterling	16,921		—
Total foreign currency forward contracts	$	40,255	$	17,468

Schedule of Foreign Exchange Contracts

The following table summarizes the fair value of the Company's outstanding foreign currency forward contracts included on the Company's condensed consolidated balance sheets:



	As of June 30, 2014			As of December 31, 2013
	(in thousands)
Fair value - assets	$	50		$	—
Fair value - liabilities	(198		)	(23		)
Net carrying value	$	(148	)	$	(23	)

Inventories (Tables)

6 Months Ended

Jun. 30, 2014

Inventory Disclosure [Abstract]

Schedule of Inventories by Type

The following table sets forth the Company’s inventories by type:



	As of June 30, 2014		As of December 31, 2013
	(in thousands)
Raw materials	$	—	$	489
Work-in-process	11,013		9,981
Finished goods	969		3,677
Total	$	11,982	$	14,147

Long-term Obligations (Tables)

6 Months Ended

Jun. 30, 2014

Long-term Debt and Capital Lease Obligations [Abstract]

Schedule of Future Minimum Lease Payments for Capital Lease

The following table sets forth the Company’s future minimum payments due under capital leases as of June 30, 2014:



Year	(in thousands)
2014	$	9,519
2015	20,792
2016	14,254
2017	13,129
2018	13,027
2019	3,047
Thereafter	—
Total payments	$	73,768
Less: amount representing interest	(9,008		)
Present value of payments	$	64,760

Stock-based Compensation Expense (Tables)

6 Months Ended

Jun. 30, 2014

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

Stock-based compensation expense by line item

During the three and six months ended June 30, 2014 and 2013, the Company recognized the following stock-based compensation expense:



	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
	(in thousands)
Stock-based compensation expense by type of award:
Stock options	$	26,985		$	29,949		$	52,112		$	49,623
Restricted stock and restricted stock units	14,020			9,732			33,013			19,110
ESPP share issuances	1,681			2,051			4,348			4,573
Less stock-based compensation expense capitalized to inventories	(242		)	(382		)	(449		)	(681		)
Total stock-based compensation expense included in costs and expenses	$	42,444		$	41,350		$	89,024		$	72,625

Stock-based compensation expense by line item:
Research and development expenses	$	27,253		$	25,740		$	60,153		$	45,089
Sales, general and administrative expenses	15,191			15,610			28,871			27,536
Total stock-based compensation expense included in costs and expenses	$	42,444		$	41,350		$	89,024		$	72,625

Unrecognized stock-based compensation expense, net of estimated forfeitures



	As of June 30, 2014
	Unrecognized Expense, Net of Estimated Forfeitures		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Stock options	$	158,362	2.33
Restricted stock and restricted stock units	$	102,006	2.14
ESPP share issuances	$	4,082	0.58

Stock options outstanding and exercisable

The following table summarizes information about stock options outstanding and exercisable at June 30, 2014:



	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)
$10.41–$20.00	368	2.01	$15.59	368	$15.59
$20.01–$30.00	889	5.42	$29.46	708	$29.35
$30.01–$40.00	4,876	5.17	$36.20	3,758	$35.73
$40.01–$50.00	3,508	8.37	$46.32	890	$46.55
$50.01–$60.00	1,348	7.34	$54.11	800	$54.63
$60.01–$70.00	129	9.15	$65.71	20	$64.33
$70.01–$80.00	2,095	9.60	$76.73	308	$74.18
$80.01–$88.18	1,336	9.02	$83.11	375	$82.53
Total	14,549	7.10	$49.77	7,227	$41.65

Restructuring Liabilities (Tables)

6 Months Ended

Jun. 30, 2014

Restructuring Cost and Reserve [Line Items]

The activities related to the restructuring liability for the three and six months ended June 30, 2014 and 2013 were as follows:



	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
	(in thousands)
Liability, beginning of the period	$	18,324		$	22,459		$	19,115		$	23,328
Cash payments	(3,960		)	(3,849		)	(7,822		)	(7,422		)
Cash received from subleases	2,689			2,666			5,378			5,331
Restructuring (income) expense	(2,117		)	776			(1,735		)	815
Liability, end of the period	$	14,936		$	22,052		$	14,936		$	22,052

Fan Pier Move Restructuring

Restructuring Cost and Reserve [Line Items]

Restructuring charges and related liability

The activities related to the restructuring liability for the three and six months ended June 30, 2014 were as follows:



	Three Months Ended June 30, 2014			Six Months Ended June 30, 2014
	(in thousands)
Liability, beginning of the period	$	3,722		$	797
Cash payments	(2,143		)	(4,377		)
Restructuring expense	1,677			6,836
Liability, end of the period	$	3,256		$	3,256

Strategic Restructuring

Restructuring Cost and Reserve [Line Items]

Restructuring charges and related liability

The activities related to the restructuring liability for the three and six months ended June 30, 2014 were as follows:



	Three Months Ended June 30, 2014			Six Months Ended June 30, 2014
	(in thousands)
Liability, beginning of the period	$	1,821		$	8,441
Cash payments	(1,199		)	(8,466		)
Restructuring expense	170			817
Liability, end of the period	$	792		$	792

Basis of Presentation and Accounting Policies (Details)	6 Months Ended
Basis of Presentation and Accounting Policies (Details)	Jun. 30, 2014 segment
Accounting Policies [Abstract]
Number of operating segments (segments)	1

Product Revenues, Net (Details) $ in Thousands	6 Months Ended
Product Revenues, Net (Details) $ in Thousands	Jun. 30, 2014 USD ($)
Product Revenue Allowance and Reserve [Roll Forward]
Product revenue allowance and reserve, beginning balance	$ 87,133
Provision related to current period sales	32,215
Adjustments related to prior period sales	7,978
Credits/payments made	(68,634)
Product revenue allowance and reserve, ending balance	58,692
Trade Allowances
Product Revenue Allowance and Reserve [Roll Forward]
Product revenue allowance and reserve, beginning balance	1,535
Provision related to current period sales	4,513
Adjustments related to prior period sales	(8)
Credits/payments made	(5,271)
Product revenue allowance and reserve, ending balance	769
Rebates, Chargebacks and Discounts
Product Revenue Allowance and Reserve [Roll Forward]
Product revenue allowance and reserve, beginning balance	68,244
Provision related to current period sales	26,464
Adjustments related to prior period sales	3,861
Credits/payments made	(57,617)
Product revenue allowance and reserve, ending balance	40,952
Product Returns
Product Revenue Allowance and Reserve [Roll Forward]
Product revenue allowance and reserve, beginning balance	15,799
Provision related to current period sales	379
Adjustments related to prior period sales	4,124
Credits/payments made	(4,160)
Product revenue allowance and reserve, ending balance	16,142
Other Incentives
Product Revenue Allowance and Reserve [Roll Forward]
Product revenue allowance and reserve, beginning balance	1,555
Provision related to current period sales	859
Adjustments related to prior period sales	1
Credits/payments made	(1,586)
Product revenue allowance and reserve, ending balance	$ 829

Collaborative Arrangements (Details) $ in Thousands	1 Months Ended			3 Months Ended					6 Months Ended		12 Months Ended
Collaborative Arrangements (Details) $ in Thousands	Jul. 31, 2014 USD ($)	Jun. 30, 2011 USD ($)	Apr. 30, 2011 USD ($)	Jun. 30, 2014 USD ($)	Dec. 31, 2013 USD ($)	Jun. 30, 2013 USD ($)	Mar. 31, 2013 USD ($)	Sep. 30, 2012 USD ($)	Jun. 30, 2014 USD ($) payment	Jun. 30, 2013 USD ($)	Dec. 31, 2006 USD ($)	Nov. 30, 2013 USD ($)
Collaborative revenues recognized
Royalty revenues (INCIVO)				$ 13,015		$ 49,120			$ 23,748	$ 92,693
Total collaborative revenues attributable to the Janssen NV collaboration				3,087		6,841			7,344	24,255
Total revenues				138,421		310,750			256,872	639,118
Collaborative revenues attributable to the CFFT collaboration				3,087		6,841			7,344	24,255
Noncontrolling Interest (Alios)
Benefit from income taxes				693		(1,799)			1,496	(132,112)
Net loss attributable to noncontrolling interest (Alios)				0		(4,547)			0	(9,158)
Janssen Pharmaceutica, N.V.
Schedule of Collaborative Arrangements
Drug development costs to be paid by collaborator (as a percent)											50.00%
Up-front license payment											$ 165,000
Deferred revenue related to up-front license payment				4,200					4,200			$ 32,100
License fee paid upon amendment of agreement					$ 152,000
Collaborative revenues recognized
Royalty revenues (INCIVO)				5,698		44,070			10,633	83,114
Up-front and amendment payments revenues				0		3,107			0	6,214
Net reimbursement for telaprevir development costs				1,483		37			2,872	9
Reimbursement for manufacturing services				0		0			0	10,299
Total collaborative revenues attributable to the Janssen NV collaboration				1,483	182,400	3,144			2,872	16,522
Total revenues				7,181		47,214			13,505	99,636
Collaborative revenues attributable to the CFFT collaboration				1,483	$ 182,400	3,144			$ 2,872	16,522
Latest expiration period for royalty obligation after first commercial sale in country unless contract is terminated earlier (in years)									10 years
Cystic Fibrosis Foundation Therapeutics Incorporated
Collaborative revenues recognized
Total collaborative revenues attributable to the Janssen NV collaboration				1,604		4,244			$ 4,472	7,803
Collaborative funding			$ 75,000
Number of years over which funding will be made (in years)			5 years
Collaborative revenues attributable to the CFFT collaboration				$ 1,604		4,244			$ 4,472	7,803
Milestone payment received							$ 9,300	$ 9,300
Number of commercial milestone payments for achievement of certain sales levels for corrector compound such as VX-809 or VX-661 (in payments) \| payment									2
Alios Bio Pharma Inc
Collaborative revenues recognized
Up-front payment		$ 60,000
Milestone payments									$ 60,000
Notice period for termination of contract after completion of clinical trials (in days)									60 days
Latest expiration period for royalty obligation after first commercial sale in country unless contract is terminated earlier (in years)									10 years
Noncontrolling Interest (Alios)
Loss before benefit from income taxes						6,824				12,121
Decrease in fair value of contingent milestone and royalty payments						80				2,820
Benefit from income taxes						(2,357)				(5,783)
Net loss attributable to noncontrolling interest (Alios)						$ 4,547				$ 9,158
Subsequent Event \| Janssen Pharmaceutica, N.V.
Collaborative revenues recognized
Up-front payment	$ 30,000

Net Loss Per Share Attributable to Vertex Common Shareholders (Details) - shares shares in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	14,549	16,802	14,549	16,802
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)	2,584	2,600	2,584	2,600

Fair Value Measurements (Details) - Recurring basis $ in Thousands	Jun. 30, 2014 USD ($)
Total
Financial assets carried at fair value:
Total	$ 922,072
Total \| Money market funds
Financial assets carried at fair value:
Cash equivalents:	123,469
Total \| Government-sponsored enterprise securities
Financial assets carried at fair value:
Marketable securities:	497,587
Total \| Commercial paper
Financial assets carried at fair value:
Marketable securities:	69,243
Total \| Corporate debt securities
Financial assets carried at fair value:
Marketable securities:	231,773
Level 1
Financial assets carried at fair value:
Total	621,056
Level 1 \| Money market funds
Financial assets carried at fair value:
Cash equivalents:	123,469
Level 1 \| Government-sponsored enterprise securities
Financial assets carried at fair value:
Marketable securities:	497,587
Level 1 \| Commercial paper
Financial assets carried at fair value:
Marketable securities:	0
Level 1 \| Corporate debt securities
Financial assets carried at fair value:
Marketable securities:	0
Level 2
Financial assets carried at fair value:
Total	301,016
Level 2 \| Money market funds
Financial assets carried at fair value:
Cash equivalents:	0
Level 2 \| Government-sponsored enterprise securities
Financial assets carried at fair value:
Marketable securities:	0
Level 2 \| Commercial paper
Financial assets carried at fair value:
Marketable securities:	69,243
Level 2 \| Corporate debt securities
Financial assets carried at fair value:
Marketable securities:	231,773
Level 3
Financial assets carried at fair value:
Total	0
Level 3 \| Money market funds
Financial assets carried at fair value:
Cash equivalents:	0
Level 3 \| Government-sponsored enterprise securities
Financial assets carried at fair value:
Marketable securities:	0
Level 3 \| Commercial paper
Financial assets carried at fair value:
Marketable securities:	0
Level 3 \| Corporate debt securities
Financial assets carried at fair value:
Marketable securities:	$ 0

Marketable Securities (Details) - USD ($) $ in Thousands	Jun. 30, 2014	Dec. 31, 2013
Summary of cash, cash equivalents and marketable securities
Amortized Cost	$ 1,219,064	$ 1,465,034
Gross Unrealized Gains	145	136
Gross Unrealized Losses	(48)	(94)
Fair Value	1,219,161	1,465,076
Total cash and cash equivalents
Summary of cash, cash equivalents and marketable securities
Amortized Cost	420,558	569,299
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	420,558	569,299
Cash and money market funds
Summary of cash, cash equivalents and marketable securities
Amortized Cost	420,558	569,299
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	420,558	569,299
Available-for-sale Securities [Member]
Summary of cash, cash equivalents and marketable securities
Amortized Cost	798,506	895,735
Gross Unrealized Gains	145	136
Gross Unrealized Losses	(48)	(94)
Fair Value	798,603	895,777
Government-sponsored enterprise securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	497,601	600,496
Gross Unrealized Gains	8	7
Gross Unrealized Losses	(22)	(53)
Fair Value	497,587	600,450
Commercial paper (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	69,144	83,384
Gross Unrealized Gains	99	109
Gross Unrealized Losses	0	0
Fair Value	69,243	83,493
Corporate debt securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	216,426	189,674
Gross Unrealized Gains	33	14
Gross Unrealized Losses	(26)	(34)
Fair Value	216,433	189,654
Corporate debt securities (due after 1 year through 5 years)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	15,335	22,181
Gross Unrealized Gains	5	6
Gross Unrealized Losses	0	(7)
Fair Value	$ 15,340	$ 22,180

Accumulated Other Comprehensive Loss (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Accumulated Other Comprehensive Income (Loss) [Roll Forward]
Balance at balance sheet date			$ (306)	$ (550)
Other comprehensive income (loss) before reclassifications			300	(680)
Amounts reclassified from accumulated other comprehensive loss			(17)	0
Total changes in other comprehensive loss	$ 274	$ (81)	283	(680)
Balance at balance sheet date	(23)	(1,230)	(23)	(1,230)
Foreign Currency Translation Adjustment
Accumulated Other Comprehensive Income (Loss) [Roll Forward]
Balance at balance sheet date			(325)	(746)
Other comprehensive income (loss) before reclassifications			353	(521)
Amounts reclassified from accumulated other comprehensive loss			0	0
Total changes in other comprehensive loss			353	(521)
Balance at balance sheet date	28	(1,267)	28	(1,267)
Unrealized Holding Gains on Marketable Securities
Accumulated Other Comprehensive Income (Loss) [Roll Forward]
Balance at balance sheet date			42	196
Other comprehensive income (loss) before reclassifications			55	(159)
Amounts reclassified from accumulated other comprehensive loss			0	0
Total changes in other comprehensive loss			55	(159)
Balance at balance sheet date	97	37	97	37
Unrealized Losses on Foreign Currency Forward Contracts
Accumulated Other Comprehensive Income (Loss) [Roll Forward]
Balance at balance sheet date			(23)	0
Other comprehensive income (loss) before reclassifications			(108)	0
Amounts reclassified from accumulated other comprehensive loss			(17)	0
Total changes in other comprehensive loss			(125)	0
Balance at balance sheet date	$ (148)	$ 0	$ (148)	$ 0

- Definition

Accumulated change in equity from transactions and other events and circumstances from non-owner sources, net of tax effect, at period end. Excludes Net Income (Loss), and accumulated changes in equity from transactions resulting from investments by owners and distributions to owners. Includes foreign currency translation items, certain pension adjustments, unrealized gains and losses on certain investments in debt and equity securities, other than temporary impairment (OTTI) losses related to factors other than credit losses on available-for-sale and held-to-maturity debt securities that an entity does not intend to sell and it is not more likely than not that the entity will be required to sell before recovery of the amortized cost basis, as well as changes in the fair value of derivatives related to the effective portion of a designated cash flow hedge.

+ References + Details

Hedging (Details) - Foreign Currency Forward Contract - USD ($) $ in Thousands	Jun. 30, 2014	Dec. 31, 2013
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair value - assets	$ 50	$ 0
Fair value - liabilities	(198)	(23)
Net carrying value	(148)	(23)
Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	40,255	17,468
Euro \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	23,334	17,468
British pound sterling \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	$ 16,921	$ 0

Inventories Inventories- Schedule of Inventories (Details) - USD ($) $ in Thousands	Jun. 30, 2014	Dec. 31, 2013
Inventory Disclosure [Abstract]
Raw materials	$ 0	$ 489
Work-in-process	11,013	9,981
Finished goods	969	3,677
Total	$ 11,982	$ 14,147

Intangible Assets and Goodwill (Details) - USD ($)	3 Months Ended				6 Months Ended
Intangible Assets and Goodwill (Details) - USD ($)	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2013	Mar. 31, 2013	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2011
Indefinite-Lived Intangible Assets [Line Items]
Intangible asset impairment charge	$ 0		$ 0		$ 0	$ 412,900,000
Deferred federal income tax expense (benefit)						$ 127,600,000
Extraordinary Item, Earnings Per Share Impact, Net						$ 1.30
Goodwill	30,992,000	$ 30,992,000	31,000,000		30,992,000	$ 31,000,000
Goodwill, period increase (decrease)	$ 0		$ 0		$ 0	0
Research and Development Arrangement \| VX-222Asset
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets				$ 0
VX-222Asset
Indefinite-Lived Intangible Assets [Line Items]
Intangible asset impairment charge				$ 412,900,000		412,900,000
Vertex
Indefinite-Lived Intangible Assets [Line Items]
Intangible asset impairment charge						$ 285,300,000
Alios Bio Pharma Inc \| Research and Development Arrangement
Indefinite-Lived Intangible Assets [Line Items]
Intangible asset impairment charge		250,600,000
Intangible assets		0					$ 250,600,000
Increase in deferred income taxes		$ 102,100,000

Convertible Senior Subordinated Notes (Details) - Convertible Senior Subordinated Notes 3.35 Percent Due 2015 - USD ($)		3 Months Ended	12 Months Ended
	Jun. 17, 2013	Jun. 30, 2013	Dec. 31, 2010
Convertible Senior Subordinated Notes
Convertible senior subordinated notes			$ 400,000,000.0
Interest rate (as a percent)			3.35%
Net proceeds from convertible debt offering			$ 391,600,000
Underwriting discount			$ 8,400,000
Conversion price (in dollars per share)		$ 48.83	$ 48.83
Original conversion rate, number of shares to be issued per $1000 of principal (in shares)			20.4794
Convertible debt principal amount, basis for exchange		$ 1,000	$ 1,000
Percent closing price needs to exceed the conversion price for at least 20 trading days within 30 consecutive trading days for provisional redemption (as a percent)		130.00%
Minimum number of days within 30 consecutive trading days the closing price needs to exceed the conversion price for provisional redemption (in days)		20 days
Total consecutive trading days during which the closing price must exceed the conversion price for at least 20 trading days for provisional redemption (in days)		30 days
Percentage of principal amount redeemed (percent)			100.00%
Amount of converted instrument		$ 399,800,000
Convertible senior subordinated notes (due 2015) conversion (shares)		8,188,448
Value of redeemed or called stock during period	$ 200,000
Redemption premium (usd per share)		$ 16.75
Converted instrument, shares issued (shares)		87,109
Interest expense		$ 6,700,000
Convertible debt with conversion feature		$ 4,200,000

Long-term Obligations (Details) ft² in Millions, $ in Millions	12 Months Ended
	Dec. 31, 2011 leases building ft²	Jun. 30, 2014 USD ($)	Dec. 31, 2013 USD ($)
Long-term Debt and Capital Lease Obligations [Abstract]
Number of leases (leases) \| leases	2
Area of leased property (in square feet) \| ft²	1.1
Number of buildings under lease agreement (buildings) \| building	2
Optional term of lease agreement (in years)	10 years
Construction in progress		$ 522.2	$ 503.4
Construction financing lease obligation		473.6	$ 440.9
Amount outstanding on line of credit		$ 33.5

- Definition

The carrying value as of the balance sheet date of the current and noncurrent portions of long-term obligations drawn from a line of credit, which is a bank's commitment to make loans up to a specific amount. Examples of items that might be included in the application of this element may consist of letters of credit, standby letters of credit, and revolving credit arrangements, under which borrowings can be made up to a maximum amount as of any point in time conditional on satisfaction of specified terms before, as of and after the date of drawdowns on the line. Includes short-term obligations that would normally be classified as current liabilities but for which (a) postbalance sheet date issuance of a long term obligation to refinance the short term obligation on a long term basis, or (b) the enterprise has entered into a financing agreement that clearly permits the enterprise to refinance the short-term obligation on a long term basis and the following conditions are met (1) the agreement does not expire within 1 year and is not cancelable by the lender except for violation of an objectively determinable provision, (2) no violation exists at the BS date, and (3) the lender has entered into the financing agreement is expected to be financially capable of honoring the agreement.

+ References + Details

Long-term Debt Obligations (Details) $ in Thousands	Jun. 30, 2014 USD ($)
Long-term Debt and Capital Lease Obligations [Abstract]
2014	$ 9,519
2015	20,792
2016	14,254
2017	13,129
2018	13,027
2019	3,047
Thereafter	0
Total payments	73,768
Less: amount representing interest	(9,008)
Present value of payments	$ 64,760

Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Stock-based compensation expense:
Less stock-based compensation expense capitalized to inventories	$ (242)	$ (382)	$ (449)	$ (681)
Total stock-based compensation expense included in costs and expenses	42,444	41,350	89,024	72,625
Stock options
Stock-based compensation expense:
Stock-based compensation expense by type of award:	26,985	29,949	52,112	49,623
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	158,362		$ 158,362
Weighted-average Recognition Period			2 years 3 months 29 days
Restricted stock and restricted stock units
Stock-based compensation expense:
Stock-based compensation expense by type of award:	14,020	9,732	$ 33,013	19,110
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	102,006		$ 102,006
Weighted-average Recognition Period			2 years 1 month 21 days
ESPP share issuances
Stock-based compensation expense:
Stock-based compensation expense by type of award:	1,681	2,051	$ 4,348	4,573
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	4,082		$ 4,082
Weighted-average Recognition Period			6 months 29 days
Research and development expenses
Stock-based compensation expense:
Total stock-based compensation expense included in costs and expenses	27,253	25,740	$ 60,153	45,089
Sales, general and administrative expenses
Stock-based compensation expense:
Total stock-based compensation expense included in costs and expenses	$ 15,191	$ 15,610	$ 28,871	$ 27,536
Maximum
Share-based Compensation Arrangement by Share-based Payment Award
Maximum percent of employees eligible for partial or full acceleration of equity awards (percent)	5.00%		5.00%

Stock-based Compensation Expense (Details 2) shares in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2014 $ / shares shares	Jun. 30, 2014 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price range, options outstanding (in shares) \| shares	14,549	14,549
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)		7 years 1 month 6 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 49.77	$ 49.77
Exercise price range, options exercisable (in shares) \| shares	7,227	7,227
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 41.65	$ 41.65
$10.41–$20.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	10.41
Exercise price, high end of range (usd per share)	$ 20.00
Exercise price range, options outstanding (in shares) \| shares	368	368
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	2 years 4 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 15.59	$ 15.59
Exercise price range, options exercisable (in shares) \| shares	368	368
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 15.59	$ 15.59
$20.01–$30.00
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)	$ 30.00
Exercise price range, options outstanding (in shares) \| shares	889	889
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	5 years 5 months 1 day
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 29.46	$ 29.46
Exercise price range, options exercisable (in shares) \| shares	708	708
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 29.35	$ 29.35
$30.01–$40.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	30.01
Exercise price, high end of range (usd per share)	$ 40.00
Exercise price range, options outstanding (in shares) \| shares	4,876	4,876
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	5 years 2 months 1 day
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 36.20	$ 36.20
Exercise price range, options exercisable (in shares) \| shares	3,758	3,758
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 35.73	$ 35.73
$40.01–$50.00
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)	$ 50.00
Exercise price range, options outstanding (in shares) \| shares	3,508	3,508
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 4 months 13 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 46.32	$ 46.32
Exercise price range, options exercisable (in shares) \| shares	890	890
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 46.55	$ 46.55
$50.01–$60.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	50.01
Exercise price, high end of range (usd per share)	$ 60.00
Exercise price range, options outstanding (in shares) \| shares	1,348	1,348
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 4 months 2 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 54.11	$ 54.11
Exercise price range, options exercisable (in shares) \| shares	800	800
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 54.63	$ 54.63
$60.01–$70.00
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)	$ 70.00
Exercise price range, options outstanding (in shares) \| shares	129	129
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	9 years 1 month 24 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 65.71	$ 65.71
Exercise price range, options exercisable (in shares) \| shares	20	20
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 64.33	$ 64.33
$70.01–$80.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	70.01
Exercise price, high end of range (usd per share)	$ 80
Exercise price range, options outstanding (in shares) \| shares	2,095	2,095
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	9 years 7 months 6 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 76.73	$ 76.73
Exercise price range, options exercisable (in shares) \| shares	308	308
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 74.18	$ 74.18
$80.01–$88.18
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)	$ 88.18
Exercise price range, options outstanding (in shares) \| shares	1,336	1,336
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	9 years 7 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 83.11	$ 83.11
Exercise price range, options exercisable (in shares) \| shares	375	375
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 82.53	$ 82.53

Sale of HIV Protease Inhibitor Royalty Stream (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2008	Jun. 30, 2014
Sale of HIV Protease Inhibitor Royalty Stream
Gross proceeds from sale of royalty rights receivable from GlaxoSmithKline	$ 160.0
Deferred Revenue Royalty Purchase Agreement		$ 53.9

Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
Income Tax Disclosure [Abstract]
Benefit from income taxes	$ 693	$ (1,799)	$ 1,496	$ (132,112)
Unrecognized tax benefits	$ 3,000		$ 3,000		$ 2,000

Restructuring Liabilities (Details) - ft² ft² in Thousands	6 Months Ended	12 Months Ended
Restructuring Liabilities (Details) - ft² ft² in Thousands	Jun. 30, 2014	Dec. 31, 2011	Dec. 31, 2003
Restructuring Cost and Reserve [Line Items]
Area of leased property (in square feet)		1,100
Kendall Restructuring
Restructuring Cost and Reserve [Line Items]
Lease term (in years)			15 years
Fan Pier Move Restructuring
Restructuring Cost and Reserve [Line Items]
Area of leased property (in square feet)	120

Restructuring Liabilities (Details 2) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Restructuring activities
Restructuring (income) expense	$ (270)	$ 776	$ 5,918	$ 815
Kendall Restructuring
Restructuring activities
Liability, beginning of the period	18,324	22,459	19,115	23,328
Cash payments	(3,960)	(3,849)	(7,822)	(7,422)
Cash received from subleases	2,689	2,666	5,378	5,331
Restructuring (income) expense	(2,117)	776	(1,735)	815
Liability, end of the period	14,936	$ 22,052	14,936	$ 22,052
Fan Pier Move Restructuring
Restructuring activities
Liability, beginning of the period	3,722		797
Cash payments	(2,143)		(4,377)
Restructuring (income) expense	1,677		6,836
Liability, end of the period	3,256		3,256
Strategic Restructuring
Restructuring activities
Liability, beginning of the period	1,821		8,441
Cash payments	(1,199)		(8,466)
Restructuring (income) expense	170		817
Liability, end of the period	$ 792		$ 792

Other Income (Expense), Net (Details) - USD ($) $ in Millions	1 Months Ended	3 Months Ended	6 Months Ended
	Apr. 30, 2014	Jun. 30, 2014	Jun. 30, 2014
Other Income and Expenses [Abstract]
Other Nonoperating Income	$ 36.7	$ 36.7	$ 36.7

Subsequent Events (Details) - Subsequent Event	Jul. 09, 2014 USD ($)
Senior Secured Term Loan
Subsequent Event [Line Items]
Face amount of term loan	$ 300,000,000
Interest rate (percent)	7.20%
Contingent interest rate (percent)	6.20%
Amount of principal repayment on quarterly installment payments through July 2016	$ 15,000,000
Amount of principal repayment on quarterly installment payments from October 2016	60,000,000
Senior Secured Term Loan Facility
Subsequent Event [Line Items]
Maximum borrowing capacity	$ 200,000,000
LIBOR \| Minimum \| Senior Secured Term Loan
Subsequent Event [Line Items]
Basis spread on variable rate (percent)	5.00%
LIBOR \| Maximum \| Senior Secured Term Loan
Subsequent Event [Line Items]
Basis spread on variable rate (percent)	7.50%