Filed pursuant to Rule 424(b)(3) Registration No. 333-37794 PROSPECTUS SUPPLEMENT NO. 2 DATED MAY 25, 2001 TO THE PROSPECTUS DATED MARCH 9, 2001 OF VERTEX PHARMACEUTICALS INCORPORATED This Prospectus Supplement No. 2 amends the information in the table under the caption "Selling Holders" in the Prospectus dated March 9, 2001, as previously amended, by deleting the information contained in the table regarding the Selling Security Holders with respect to the principal amount of notes and common stock of Vertex Pharmaceuticals Incorporated and substituting therefor the following table: PRINCIPAL AMOUNT NUMBER OF SHARES OF COMMON STOCK OF NOTES OWNED ISSUABLE UPON CONVERSION OF AND OFFERED (1) BENEFICIALLY THE NOTES THAT MAY BE OFFERED --------------- ------------------------------------------ NAME OF SECURITY HOLDER AAM/Zazone Institutional Income Fund L.P. $ 850,000 9,213 AFTRA Health Fund $300,000 3,251 AIG/National Union Fire Insurance $ 975,000 10,567 Alexandra Global Investment Fund 1 Ltd $ 3,000,000 32,516 AllState Insurance Company $ 2,000,000 21,677 Alpine Associates $ 4,600,000 49,859 Alpine Partners, L.P $ 700,000 7,587 American Motorist Insurance Company $ 763,000 8,270 Arapahoe County Colorado $ 75,000 812 Arkansas Teachers Retirement $ 5,850,000 63,407 Argent Classic Arbitrage fund (Bermuda) L.P. $ 4,400,000 47,691 Argent Classic Convertible Arbitrage Fund (Bermuda) L.P $ 5,400,000 58,530 Argent Classic Convertible Arbitrage Fund L.P $ 1,600,000 17,342 -1-
Associated Electric & Gas Insurance Services Limited $ 400,000 4,335 Attorney's Title Insurance Fund, Inc $ 500,000 5,419 Bank Austria Cayman Island, L $ 5,800,000 62,865 Baptist Health Southern Florida $ 367,000 3,977 Bear Stearns $ 5,000,000 54,195 BNP Cooper Neff Convertible Strategies Fund, L.P. $ 188,000 2,037 Boilermakers Blacksmith Pension Trust $ 1,650,000 17,884 Boston Museum of Fine Arts $ 151,000 1,636 Boulder II Limited $ 2,850,000 30,891 BP Amoco PLC Master Trust $ 1,758,000 19,054 California Public Employees Retirement System Nominee Name $ 3,000,000 32,516 Surfboard & Co. CALAMOS Market Neutral Fund-CALAMOS Investment Trust $ 1,670,000 18,101 Canyon Value Realization (Cayman) Ltd. $ 11,000,000 119,228 CFFX, LLC $ 2,000,000 21,677 CIBC World Markets $ 6,000,000 65,033 City of New Orleans $ 315,000 3,414 City University of New York $ 185,000 2,005 Clinton Riverside Convertible Portfolio Limited $ 4,500,000 48,775 Conseco Fund Group - Convertible Securities Fund $ 3,250,000 35,226 Conseco Health Insurance Company - Convertible $ 1,500,000 16,258 Conseco Senior Health Insurance Company Convertible $ 1,500,000 16,258 -2-
Conseco Variable Insurance Company - Convertible $ 750,000 8,129 Consulting Group Capital Markets Funds $ 450,000 4,877 Cova Bond Debenture Fund $ 500,000 5,419 Credit Suisse First Boston Corporation $ 5,000,000 54,196 CSFB Convertible & Quantitative Strategies $ 1,000,000 10,838 D.E. Shaw Investments, L.P. $ 1,500,000 16,258 D.E. Shaw Valence, L.P $ 5,500,000 59,614 Deephaven Domestic Convertible Trading Co $ 1,000,000 10,838 Delphi Financial Group, Inc. $500,000 5,419 Delaware PERS $ 1,840,000 19,943 Deutsche Bank Securities $ 48,500,000 525,688 Elf Aquitaine $ 200,000 2,167 Engineers Joint Pension Fund $ 621,000 6,730 Employee Benefit Convertible Securities Fund $ 200,000 2,167 Enterprise Convertible Securities Fund $108,000 1,170 Franklin and Marshall College $ 245,000 2,665 First Republic Bank $ 225,000 2,438 Fuji U. S. Income Open $ 500,000 5,419 Gaia Offshore Master Fund Ltd. $ 2,500,000 27,097 Goldman Sachs and Company $ 52,000 564 Grady Hospital Foundation $ 161,000 1,745 Granville Capital Corporation $ 6,000,000 65,033 Hamilton Partners Limited $ 4,000,000 43,355 HFR Master Fund, Ltd $ 130,000 1,409 Highbridge International LLC $ 18,000,000 195,100 -3-
Hotel Union & Hotel Industry of Hawaii $ 980,000 10,622 ICI American Holdings Trust $ 980,000 10,622 Independence Blue Cross $ 138,000 1,495 Island Holdings $ 60,000 650 ITG, Inc $ 203,000 2,200 James Cambell Corporation $386,000 4,183 JAS Securities $2,250,000 24,387 J.P. Morgan Securities, Inc. $ 10,950,000 118,686 Jeffries & Company Inc. $ 11,000 119 Kentfield Trading, Ltd. $ 3,760,000 40,754 Lazard Freres & Co. LLC $ 1,000,000 10,838 Lehman Brothers International Europe $ 1,550,000 16,800 Lipper Convertibles Series II, L.P.'s $ 1,875,000 20,323 Lipper Offshore Convertibles, L.P. $ 1,875,000 20,323 Lipper Offshore Convertibles, L.P. #2 $ 750,000 8,129 Lippers Convertibles, L.P.'s (Class B) $ 436,000 4,725 Local Initiatives Union $ 72,000 780 Lord Abbett Bond Debenture Fund $ 2,000,000 21,677 Lord Abbett Bond Debenture Fund $ 500,000 5,419 Lumberman's Mutual Casualty $ 643,000 6,969 Mainstay Convertible Fund $ 5,000,000 54,194 Mainstay VP Convertible Portfolio $ 1,000,000 10,838 McMahan Securities $2,150,000 23,303 Morgan Stanley & Co. $ 5,000,000 54,194 Nabisco Corporation $45,000 487 -4-
Nalco Chemical Company $ 335,000 3,631 Nations Convertible Securities Fund $ 3,300,000 35,768 New Orleans Firefighters Pension/Relief Fund $ 166,000 1,799 New York Life Separate Account #7 $600,000 6,503 New York Life Insurance and Annuity Corporation $ 17,000,000 184,262 New York Life Insurance Company $ 19,500,000 211,359 Nicholas Applegate Convertible Fund $ 2,107,000 22,837 Occidental Petroleum Corporation $ 305,000 3,305 Onex Industrial Partners $ 1,850,000 20,052 Onyx Capital Management, LLC $ 5,000,000 54,195 Oxford, Lord Abbett & Co, $ 800,000 8,671 Pacific Life Insurance Company $ 500,000 5,419 Pebble Capital Inc. $ 700,000 7,587 Penn Treaty Network America Insurance Company $ 295,000 3,197 Peoples Benefit Life Insurance Company Teamsters $ 3,725,000 40,375 PGEP IV, LLC $ 113,000 1,224 Physicians Life $ 487,000 5,278 PIMCO Convertible Bond $ 3,000,000 32,516 Police & Fireman Retirement System of the City $850,000 9,213 Of Detroit Pro Mutual $ 1,171,000 12,692 Putnam Investment Management Inc. on behalf of: Putnam $ 190,000 2,059 Asset Allocation Funds-Balanced Portfolio -5-
Putnam Investment Management, Inc. on behalf of: Putnam $ 130,000 1,409 Asset Allocation Funds - Conservative Portfolio Putnam Investment Management, Inc. on behalf of: Putnam $ 1,000,000 10,838 Convertible Income-Growth Trust Putnam Investment Management, Inc. on behalf of: Putnam $ 70,000 758 Convertible Opportunities and Income Trust Quattro Global Capital, LLC $ 1,500,000 16,258 Quattro Global Capital, LLC $ 1,500,000 16,258 Ramius Capital Group Holdings, Ltd. $ 900,000 9,755 Raytheon Master Pension Trust $ 829,000 8,985 RCG Latitude Master Fund, Ltd. $ 300,00 3,251 RJ Reynolds (RJR) $ 143,000 1,549 Robertson Stephens $30,000,000 325,168 San Diego City Retirement $ 1,247,000 13,516 San Diego County Convertible $ 2,674,000 28,983 San Diego Employees Retirement Association $ 1,900,000 20,593 Salomon Brothers Asset Management Inc. $31,750,000 344,136 Screen Actors Guild Convertible $ 662,000 7,175 SG Cowen Securities $9,000,000 97,550 Shell Pension Trust $ 642,000 6,958 Silvercreek Limited Partnership $ 1,100,000 11,923 Southern Farm Bureau Life Insurance $ 770,000 8,345 State of Maryland Retirement Agency $ 3,880,000 42,055 State of Oregon Equity $ 5,975,000 64,762 State Street Bank custodian For GE Pension Trust $ 1,805,000 19,564 -6-
Starvest Combined Portfolio $ 1,185,000 12,844 Teachers Insurance and Annuity Association $ 4,000,000 43,355 The Estate of James Campbell $ 509,000 5,517 The Putnam Advisory Company, Inc. on behalf of: University $ 30,000 325 of Rochester The Putnam Advisory Company, Inc. on behalf of: $ 50,000 541 Parker-Hammifin Corporation The Putnam Advisory Company, Inc. on behalf of: Museum of $ 30,000 325 Fine Arts, Boston The Putnam Advisory Company, Inc. on behalf of: ProMutual $ 100,000 1,083 TQA Master Fund $ 950,000 10,296 TQA Master Plus Fund, Ltd. $ 1,000,000 10,838 Tracor, Inc. Employees Retirement Plan $ 172,000 1,846 Transamerica Life Insurance and Annuity Company $ 8,000,000 86,711 Transamerica Premier Balanced Fund $ 1,000,000 10,838 UBS O'Connor LLC, F/B/O UBS Global Equity Arbitrage Master $ 500,000 5,419 Limited Value Realization Fund B, LP $450,000 4,877 Value Realization Fund, LP $ 8,000,000 86,711 Viacom Inc. Pension Plan Master Trust $ 68,000 737 Wake Forest University $ 1,163,000 12,605 Writers Guild Convertible $ 385,000 4,172 Wyoming State Treasurer $ 1,329,000 14,404 Zeneca Holdings Trust $765,000 8,291 Zurich HFR Master Hedge Fund Index Ltd $ 100,000 1,083 Zurich HFR Calamos Holding Limited $ 80,000 867 Zurich HFR Master Hedge Fund Index Ltd $ 200,000 2,167 -7-
1976 Distribution Trust FBO A.R. Lauder/Zinterhofer $ 21,000 227 1976 Distribution Trust FBO Jane A. Lauder $ 21,000 227 (1) The number of securities beneficially owned is determined under the rules of the SEC and the information is not necessarily indicative of beneficial ownership for any other purpose. Under those rules, beneficial ownership includes any securities as to which the individual has sole or shared voting power or investment power and also any securities which the individual has the right to acquire within 60 days after the date the selling holder provided this information, through the exercise of any stock option or other right. The inclusion in the table of securities, however, does not constitute an admission that the selling holders are direct or indirect beneficial owners of those securities. The selling holders have sole voting power and investment power with respect to all securities of capital stock listed as owned by the selling holders. This Prospectus Supplement No. 2 should be read in conjunction with the Prospectus dated March 9, 2001. -8-