<PAGE>

                                                                     EXHIBIT 4.2

                      RESALE REGISTRATION RIGHTS AGREEMENT


                                      among


                      VERTEX PHARMACEUTICALS INCORPORATED,


                                       and


                               MERRILL LYNCH & CO.
               MERRILL LYNCH, PIERCE, FENNER & SMITH INCORPORATED
                            BEAR, STEARNS & CO. INC.
                     CREDIT SUISSE FIRST BOSTON CORPORATION
                       FLEETBOSTON ROBERTSON STEPHENS INC.
                        SG COWEN SECURITIES CORPORATION,
              as Representatives of the several Initial Purchasers


                              Dated March 14, 2000


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     Resale Registration Rights Agreement (this "Agreement"), dated March 14,
2000, among Vertex Pharmaceuticals Incorporated, a Massachusetts corporation
(together with any successor entity, the "Issuer"), and Merrill Lynch & Co.,
Merrill Lynch, Pierce, Fenner & Smith Incorporated ("Merrill Lynch"), Bear,
Stearns & Co. Inc., Credit Suisse First Boston Corporation, FleetBoston
Robertson Stephens Inc. and SG Cowen Securities Corporation, as Representatives
of the several Initial Purchasers (collectively, the "Initial Purchasers").

     Pursuant to the Purchase Agreement, dated March 8, 2000, between the Issuer
and the Initial Purchasers (the "Purchase Agreement"), the Initial Purchasers
have agreed to purchase from the Issuer $175,000,000 ($201,250,000 if the
Initial Purchasers exercise the over-allotment option in full) in aggregate
principal amount of 5% Convertible Subordinated Notes due 2007 (the "Notes").
The Notes will be convertible into fully paid, nonassessable common stock, par
value $.01 per share, of the Issuer (the "Common Stock") on the terms, and
subject to the conditions, set forth in the Indenture (as defined herein). To
induce the Initial Purchasers to purchase the Notes, the Issuer has agreed to
provide the registration rights set forth in this Agreement pursuant to the
Purchase Agreement.

     The parties hereby agree as follows:

     1. DEFINITIONS. As used in this Agreement, the following capitalized terms
shall have the following meanings:

     ADVICE: As defined in Section 4(c)(ii) hereof.

     BUSINESS DAY: A day other than a Saturday or Sunday or any federal holiday
in the United States.

     COMMISSION: Securities and Exchange Commission.

     COMMON STOCK: As defined in the preamble hereto.

     DAMAGES PAYMENT DATE: Each Interest Payment Date. For purposes of this
Agreement, if no Notes are outstanding, "DAMAGES PAYMENT DATE" shall mean each
March 14 and September 14.

     EFFECTIVENESS PERIOD: As defined in Section 2(a)(iii) hereof.

     EFFECTIVENESS TARGET DATE: As defined in Section 2(a)(ii) hereof.

     EXCHANGE ACT: Securities Exchange Act of 1934, as amended.


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     HOLDER: A Person who owns, beneficially or otherwise, Transfer Restricted
Securities.

     INDENTURE: The Indenture, dated as of March 14, 2000, between the Issuer
and State Street Bank and Trust Company, as trustee, pursuant to which the Notes
are to be issued, as such Indenture is amended, modified or supplemented from
time to time in accordance with the terms thereof.

     INITIAL PURCHASERS: As defined in the preamble hereto.

     INTEREST PAYMENT DATE: As defined in the Indenture.

     ISSUER: As defined in the preamble hereto.

     LIQUIDATED DAMAGES: As defined in Section 3(a) hereof.

     MAJORITY OF HOLDERS: Holders holding over 50% of the aggregate principal
amount of Notes outstanding; PROVIDED that, for purpose of this definition, a
holder of shares of Common Stock which constitute Transfer Restricted Securities
and were issued upon conversion of the Notes shall be deemed to hold an
aggregate principal amount of Notes (in addition to the aggregate principal
amount of Notes held by such holder) equal to the aggregate principal amount of
Notes converted by such Holder into such shares of Common Stock.

     NASD: National Association of Securities Dealers, Inc.

     NOTES: As defined in the preamble hereto.

     PERSON: An individual, partnership, corporation, unincorporated
organization, trust, joint venture or a government or agency or political
subdivision thereof.

     PROSPECTUS: The prospectus included in a Shelf Registration Statement, as
amended or supplemented by any prospectus supplement and by all other amendments
thereto, including post-effective amendments, and all material incorporated by
reference into such Prospectus.

     QUESTIONNAIRE DEADLINE: As defined in Section 2(b) hereof.

     RECORD HOLDER: With respect to any Damages Payment Date, each Person who is
a Holder on the record date with respect to the Interest Payment Date on which
such Damages Payment Date shall occur. In the case of a Holder of shares of
Common Stock issued upon conversion of the Notes, "RECORD HOLDER" shall mean
each Person who is a


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Holder of shares of Common Stock which constitute Transfer Restricted Securities
on the March 1 or September 1 immediately preceding the Damages Payment Date.

     REGISTRATION DEFAULT: As defined in Section 3(a) hereof.

     SALE NOTICE: As defined in Section 4(e) hereof.

     SECURITIES ACT: Securities Act of 1933, as amended.

     SHELF FILING DEADLINE: As defined in Section 2(a)(i) hereof.

     SHELF REGISTRATION STATEMENT: As defined in Section 2(a)(i) hereof.

     SUSPENSION PERIOD: As defined in Section 4(b)(i) hereof.

     TIA: Trust Indenture Act of 1939, as in effect on the date the Indenture is
qualified under the TIA.

     TRANSFER RESTRICTED SECURITIES: Each Note and each share of Common Stock
issued upon conversion of Notes until the earlier of:

          (i) the date on which such Note or such share of Common Stock issued
     upon conversion has been effectively registered under the Securities Act
     and disposed of in accordance with the Shelf Registration Statement;

          (ii) the date on which such Note or such share of Common Stock issued
     upon conversion is transferred in compliance with Rule 144 under the
     Securities Act or may be sold or transferred pursuant to Rule 144(k) under
     the Securities Act (or any other similar provision then in force); or

          (iii) the date on which such Note or such share of Common Stock issued
     upon conversion ceases to be outstanding (whether as a result of
     redemption, repurchase and cancellation, conversion or otherwise).

     UNDERWRITTEN REGISTRATION OR UNDERWRITTEN OFFERING: A registration in which
securities of the Issuer are sold to an underwriter for reoffering to the
public.

     2. SHELF REGISTRATION.

     (a) The Issuer shall:

          (i) not later than 90 days after the date hereof (the "Shelf Filing
     Deadline"), cause to be filed a registration statement pursuant to Rule 415
     under


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     the Securities Act (the "Shelf Registration Statement"), which Shelf
     Registration Statement shall provide for resales of all Transfer Restricted
     Securities held by Holders that have provided the information required
     pursuant to the terms of Section 2(b) hereof;

          (ii) use its best efforts to cause the Shelf Registration Statement to
     be declared effective by the Commission as promptly as practicable, but in
     no event later than 150 days after the date hereof (the "Effectiveness
     Target Date"); and

          (iii) use its best efforts to keep the Shelf Registration Statement
     continuously effective, supplemented and amended as required by the
     provisions of Section 4(b) hereof to the extent necessary to ensure that
     (A) it is available for resales by the Holders of Transfer Restricted
     Securities entitled to the benefit of this Agreement and (B) conforms with
     the requirements of this Agreement and the Securities Act and the rules and
     regulations of the Commission promulgated thereunder as announced from time
     to time for a period (the "Effectiveness Period") of:

               (1) two years following the last date of original issuance of
          Notes; or

               (2) such shorter period that will terminate when (x) all of the
          Holders of Transfer Restricted Securities are able to sell all
          Transfer Restricted Securities immediately without restriction
          pursuant to Rule 144(k) under the Securities Act or any successor rule
          thereto, (y) when all Transfer Restricted Securities have ceased to be
          outstanding (whether as a result of redemption, repurchase and
          cancellation, conversion or otherwise) or (z) all Transfer Restricted
          Securities registered under the Shelf Registration Statement have been
          sold.

     (b) No Holder may include any of its Transfer Restricted Securities in the
Shelf Registration Statement pursuant to this Agreement unless such Holder
furnishes to the Issuer in writing, prior to or on the 20th Business Day after
receipt of a request therefor (the "Questionnaire Deadline"), such information
as the Issuer may reasonably request for use in connection with the Shelf
Registration Statement or the Prospectus or preliminary Prospectus included
therein and in any application to be filed with or under state securities laws.
In connection with all such requests for information from Holders, the Issuer
shall notify such Holders of the requirements set forth in the preceding
sentence. No Holder shall be entitled to Liquidated Damages pursuant to Section
3 hereof unless such Holder shall have provided all such reasonably requested
information prior to or on the Questionnaire Deadline.


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<PAGE>

     3. LIQUIDATED DAMAGES.

     (a) If:

          (i) the Shelf Registration Statement is not filed with the Commission
     prior to or on the Shelf Filing Deadline;

          (ii) the Shelf Registration Statement has not been declared effective
     by the Commission prior to or on the Effectiveness Target Date;

          (iii) subject to the provisions of Section 4(b)(i) hereof, the Shelf
     Registration Statement is filed and declared effective but, during the
     Effectiveness Period, shall thereafter cease to be effective or fail to be
     usable for its intended purpose without being succeeded within five
     Business Days by a post-effective amendment to the Shelf Registration
     Statement or a report filed with the Commission pursuant to Section 13(a),
     13(c), 14 or 15(d) of the Exchange Act that cures such failure and, in the
     case of a post-effective amendment, is itself immediately declared
     effective; or

          (iv) prior to or on the 45th or 60th day, as the case may be, of any
     Suspension Period, such suspension has not been terminated,

          (each such event referred to in foregoing clauses (i) through (iv), a
          "Registration Default"), the Issuer hereby agrees to pay liquidated
          damages ("Liquidated Damages") with respect to the Transfer Restricted
          Securities from and including the day following the Registration
          Default to but excluding the day on which the Registration Default has
          been cured:

               (A) in respect of the Notes, to each holder of Notes, (x) with
          respect to the first 90-day period during which a Registration Default
          shall have occurred and be continuing, in an amount per year equal to
          an additional 0.25% of the principal amount of the Notes and (y) with
          respect to the period commencing on the 91st day following the day the
          Registration Default shall have occurred and be continuing, in an
          amount per year equal to an additional 0.50% of the principal amount
          of the Notes; PROVIDED that in no event shall Liquidated Damages
          accrue at a rate per year exceeding 0.50% of the principal amount of
          the Notes; and

               (B) in respect of any shares of Common Stock, to each holder of
          shares of Common Stock issued upon conversion of Notes, (x) with
          respect to the first 90-day period in which a Registration Default
          shall have occurred and be continuing, in an amount per year equal to
          0.25% of


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          the principal amount of the converted Notes and (y) with respect to
          the period commencing the 91st day following the day the Registration
          Default shall have occurred and be continuing, in an amount per year
          equal to 0.50% of the principal amount of the converted Notes;
          PROVIDED that in no event shall Liquidated Damages accrue at a rate
          per year exceeding 0.50% of the principal amount of the converted
          Notes.

     (b) All accrued Liquidated Damages shall be paid in arrears to Record
Holders by the Issuer on each Damages Payment Date by wire transfer of
immediately available funds or by federal funds check. Following the cure of all
Registration Defaults relating to any particular Note or share of Common Stock,
the accrual of Liquidated Damages with respect to such Note or share of Common
Stock will cease.

     All obligations of the Issuer set forth in this Section 3 that are
outstanding with respect to any Transfer Restricted Security at the time such
security ceases to be a Transfer Restricted Security shall survive until such
time as all such obligations with respect to such Transfer Restricted Security
shall have been satisfied in full.

     The Liquidated Damages set forth above shall be the exclusive monetary
remedy available to the Holders for such Registration Default.

     4. REGISTRATION PROCEDURES.

     (a) In connection with the Shelf Registration Statement, the Issuer shall
comply with all the provisions of Section 4(b) hereof and shall use its best
efforts to effect such registration to permit the sale of the Transfer
Restricted Securities being sold in accordance with the intended method or
methods of distribution thereof, and pursuant thereto, shall as expeditiously as
possible prepare and file with the Commission a Shelf Registration Statement
relating to the registration on any appropriate form under the Securities Act.

     (b) In connection with the Shelf Registration Statement and any Prospectus
required by this Agreement to permit the sale or resale of Transfer Restricted
Securities, the Issuer shall:

          (i) Subject to any notice by the Issuer in accordance with this
     Section 4(b) of the existence of any fact or event of the kind described in
     Section 4(b)(iii)(D), use its best efforts to keep the Shelf Registration
     Statement continuously effective during the Effectiveness Period. Upon the
     occurrence of any event that would cause the Shelf Registration Statement
     or the Prospectus contained therein (A) to contain a material misstatement
     or omission or (B) not be effective and usable for resale of Transfer
     Restricted Securities during the


                                       6
<PAGE>

     Effectiveness Period, the Issuer shall file - promptly an appropriate
     amendment to the Shelf Registration Statement or a report filed with the
     Commission pursuant to Section 13(a), 13(c), 14 or 15(d) of the Exchange
     Act, in the case of clause (A), correcting any such misstatement or
     omission, and, in the case of either clause (A) or (B), use its best
     efforts to cause any such amendment to be declared effective and the Shelf
     Registration Statement and the related Prospectus to become usable for
     their intended purposes as soon as practicable thereafter. Notwithstanding
     the foregoing, the Issuer may suspend the effectiveness of the Shelf
     Registration Statement by written notice to the Holders for a period not to
     exceed an aggregate of 45 days in any 90-day period (each such period, a
     "Suspension Period") if:

               (x) an event occurs and is continuing as a result of which the
          Shelf Registration Statement would, in the Issuer's reasonable
          judgment, contain an untrue statement of a material fact or omit to
          state a material fact required to be stated therein or necessary to
          make the statements therein not misleading; and

               (y) the Issuer reasonably determines that the disclosure of such
          event at such time would have a material adverse effect on the
          business of the Issuer (and its subsidiaries, if any, taken as a
          whole);

     PROVIDED, that in the event the disclosure relates to a previously
     undisclosed proposed or pending material business transaction, the
     disclosure of which would impede the Issuer's ability to consummate such
     transaction, the Issuer may extend a Suspension Period from 45 days to 60
     days; PROVIDED, HOWEVER, that Suspension Periods shall not exceed an
     aggregate of 90 days in any 360-day period.

          (ii) Prepare and file with the Commission such amendments and
     post-effective amendments to the Shelf Registration Statement as may be
     necessary to keep the Shelf Registration Statement effective during the
     Effectiveness Period; cause the Prospectus to be supplemented by any
     required Prospectus supplement, and as so supplemented to be filed pursuant
     to Rule 424 under the Securities Act, and to comply fully with the
     applicable provisions of Rules 424 and 430A under the Securities Act in a
     timely manner; and comply with the provisions of the Securities Act with
     respect to the disposition of all securities covered by the Shelf
     Registration Statement during the applicable period in accordance with the
     intended method or methods of distribution by the sellers thereof set forth
     in the Shelf Registration Statement or Prospectus supplement.

          (iii) Advise the selling Holders, Merrill Lynch, as representative of
     the Initial Purchasers, and the underwriter(s), if any, promptly (but in
     any event


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     within five Business Days) and, if requested by such Persons, confirm such
     advice in writing:

               (A) with respect to the Shelf Registration Statement or any
          post-effective amendment thereto, when the same has become effective,
          and when the Prospectus or any Prospectus supplement or post-effective
          amendment has been filed,

               (B) of any request by the Commission for amendments to the Shelf
          Registration Statement or amendments or supplements to the Prospectus
          or for additional information relating thereto,

               (C) of the issuance by the Commission of any stop order
          suspending the effectiveness of the Shelf Registration Statement under
          the Securities Act or of the suspension by any state securities
          commission of the qualification of the Transfer Restricted Securities
          for offering or sale in any jurisdiction, or the initiation of any
          proceeding for any of the preceding purposes, or

               (D) of the existence of any fact or the happening of any event,
          during the Effectiveness Period, that makes any statement of a
          material fact made in the Shelf Registration Statement or the
          Prospectus, any amendment or supplement thereto, or any document
          incorporated by reference therein untrue, or that requires the making
          of any additions to or changes in the Shelf Registration Statement or
          the Prospectus in order to make the statements therein not misleading.

     If at any time the Commission shall issue any stop order suspending the
     effectiveness of the Shelf Registration Statement, or any state securities
     commission or other regulatory authority shall issue an order suspending
     the qualification or exemption from qualification of the Transfer
     Restricted Securities under state securities or Blue Sky laws, the Issuer
     shall use its reasonable best efforts to obtain the withdrawal or lifting
     of such order at the earliest possible time.

          (iv) Furnish to each of the selling Holders, each Initial Purchaser
     and each of the underwriter(s), if any, before filing with the Commission,
     a copy of the Shelf Registration Statement and copies of any Prospectus
     included therein or any amendments or supplements to the Shelf Registration
     Statement or Prospectus (other than documents incorporated by reference
     after the initial filing of the Shelf Registration Statement), which
     documents will be subject to the review of such Holders, Initial Purchasers
     and underwriter(s), if any, for a period of at least ten



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     Business Days, and the Issuer will not file any Shelf Registration
     Statement or Prospectus or any amendment or supplement to the Shelf
     Registration Statement or Prospectus (other than documents incorporated by
     reference) to which a selling Holder of Transfer Restricted Securities
     covered by the Shelf Registration Statement, Merrill Lynch, as
     representative of the Initial Purchasers, or the underwriter(s), if any,
     shall reasonably object within five Business Days after the receipt
     thereof. A selling Holder, Merrill Lynch, as representative of the Initial
     Purchasers, or an underwriter, if any, shall be deemed to have reasonably
     objected to such filing if the Shelf Registration Statement, amendment,
     Prospectus or supplement, as applicable, as proposed to be filed, contains
     a material misstatement or omission. Notwithstanding the foregoing, the
     Issuer shall not be required to furnish the selling Holders with any
     amendment or supplement to the Shelf Registration Statement or Prospectus
     filed solely to reflect changes to the amount of Notes held by any
     particular Holder at the request of such Holder or immaterial revisions to
     the information contained therein.

          (v) Make available at reasonable times for inspection by one or more
     representatives of the selling Holders, designated in writing by a Majority
     of Holders whose Transfer Restricted Securities are included in the Shelf
     Registration Statement, any underwriter participating in any distribution
     pursuant to the Shelf Registration Statement and any attorney or accountant
     retained by such selling Holders or any of the underwriter(s), all
     financial and other records, pertinent corporate documents and properties
     of the Issuer as shall be reasonably necessary to enable them to exercise
     any applicable due diligence responsibilities, and cause the Issuer's
     officers, directors, managers and employees to supply all information
     reasonably requested by any such representative or representatives of the
     selling Holders, underwriter, attorney or accountant in connection with the
     Shelf Registration Statement after the filing thereof and before its
     effectiveness; PROVIDED, HOWEVER, that any information designated by the
     Issuer as confidential at the time of delivery of such
     information shall be kept confidential by the recipient thereof.

          (vi) If requested by any selling Holders, Merrill Lynch, as
     representative of the Initial Purchasers, or the underwriter(s), if any,
     promptly incorporate in the Shelf Registration Statement or Prospectus,
     pursuant to a supplement or post-effective amendment if necessary, such
     information as such selling Holders, Merrill Lynch, as representative of
     the Initial Purchasers, and such underwriter(s), if any, may reasonably
     request to have included therein, including, without limitation: (1)
     information relating to the "Plan of Distribution" of the Transfer
     Restricted Securities, (2) - - information with respect to the principal
     amount of Notes or number of shares of Common Stock being sold to such
     underwriter(s), (3) the purchase - price being paid therefor and (4) any
     other


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     terms of the offering of the Transfer Restricted Securities to be sold in
     such offering; and make all - required filings of such Prospectus
     supplement or post-effective amendment as soon as reasonably practicable
     after the Issuer is notified of the matters to be incorporated in such
     Prospectus supplement or post-effective amendment. Notwithstanding the
     foregoing, following the effective date of the Shelf Registration
     Statement, the Issuer shall not be required to file more than one such
     supplement or post-effective amendment to reflect changes in the amount of
     Notes held by any particular Holder at the request of such Holder in any
     30-day period.

          (vii) Furnish to each selling Holder, each Initial Purchaser and each
     of the underwriter(s), if any, without charge, at least one copy of the
     Shelf Registration Statement, as first filed with the Commission, and of
     each amendment thereto (and any documents incorporated by reference therein
     or exhibits thereto (or exhibits incorporated in such exhibits by
     reference) as such Person may request).

          (viii) Deliver to each selling Holder, each Initial Purchaser and each
     of the underwriter(s), if any, without charge, as many copies of the
     Prospectus (including each preliminary prospectus) and any amendment or
     supplement thereto as such Persons reasonably may request; subject to any
     notice by the Issuer in accordance with this Section 4(b) of the existence
     of any fact or event of the kind described in Section 4(b)(iii)(D), the
     Issuer hereby consents to the use of the Prospectus and any amendment or
     supplement thereto by each of the selling Holders and each of the
     underwriter(s), if any, in connection with the offering and the sale of the
     Transfer Restricted Securities covered by the Prospectus or any amendment
     or supplement thereto.

          (ix) If an underwriting agreement is entered into and the registration
     is an Underwritten Registration, the Issuer shall:

               (A) upon request, furnish to each selling Holder and each
          underwriter, if any, in such substance and scope as they may
          reasonably request and as are customarily made by issuers to
          underwriters in primary underwritten offerings, upon the date of
          closing of any sale of Transfer Restricted Securities in an
          Underwritten Registration:

                    (1) a certificate, dated the date of such closing, signed by
               the Chief Financial Officer of the Issuer and confirming, as of
               the date thereof, the matters set forth in Section 5(c) of the
               Purchase Agreement and such other matters as such parties may
               reasonably request;


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                    (2) opinions, each dated the date of such closing, of
               counsel to the Issuer covering such of the matters set forth in
               the exhibits to the Purchase Agreement referred to in Section
               5(a) thereof as are customarily covered in legal opinions to
               underwriters in connection with primary underwritten offerings of
               securities; and

                    (3) customary comfort letters, dated the date of such
               closing, from the Issuer's independent certified public
               accountants (and from any other accountants whose report is
               contained or incorporated by reference in the Shelf Registration
               Statement), in the customary form and covering matters of the
               type customarily covered in comfort letters to underwriters in
               connection with primary underwritten offerings of securities;

               (B) set forth in full in the underwriting agreement, if any,
          indemnification provisions and procedures which provide rights no less
          protective than those set forth in Section 6 hereof with respect to
          all parties to be indemnified; and

               (C) deliver such other documents and certificates as may be
          reasonably requested by such parties to evidence compliance with
          clause (A) above and with any customary conditions contained in the
          underwriting agreement or other agreement entered into by the selling
          Holders pursuant to this clause (ix).

          (x) Before any public offering of Transfer Restricted Securities,
     cooperate with the selling Holders, the underwriter(s), if any, and their
     respective counsel in connection with the registration and qualification of
     the Transfer Restricted Securities under the securities or Blue Sky laws of
     such jurisdictions as the selling Holders or underwriter(s), if any, may
     reasonably request and do any and all other acts or things necessary or
     advisable to enable the disposition in such jurisdictions of the Transfer
     Restricted Securities covered by the Shelf Registration Statement;
     PROVIDED, HOWEVER, that the Issuer shall not be required (A) to register or
     qualify as a foreign corporation or a dealer of securities where it is not
     now so qualified or to take any action that would subject it to the service
     of process in any jurisdiction where it is not now so subject or (B) to
     subject itself to taxation in any such jurisdiction if it is not now so
     subject.

          (xi) Cooperate with the selling Holders and the underwriter(s), if
     any, to facilitate the timely preparation and delivery of certificates
     representing Transfer Restricted Securities to be sold and not bearing any
     restrictive legends


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     (unless required by applicable securities laws); and enable such Transfer
     Restricted Securities to be in such denominations and registered in such
     names as the Holders or the underwriter(s), if any, may request at least
     two Business Days before any sale of Transfer Restricted Securities made by
     such underwriter(s).

          (xii) Use its best efforts to cause the Transfer Restricted Securities
     covered by the Shelf Registration Statement to be registered with or
     approved by such other U.S. governmental agencies or authorities as may be
     necessary to enable the seller or sellers thereof or the underwriter(s), if
     any, to consummate the disposition of such Transfer Restricted Securities.

          (xiii) Subject to Section 4(b)(i) hereof, if any fact or event
     contemplated by Section 4(b)(iii)(D) hereof shall exist or have occurred,
     use its reasonable best efforts to prepare a supplement or post-effective
     amendment to the Shelf Registration Statement or related Prospectus or any
     document incorporated therein by reference or file any other required
     document so that, as thereafter delivered to the purchasers of Transfer
     Restricted Securities, the Prospectus will not contain an untrue statement
     of a material fact or omit to state any material fact required to be stated
     therein or necessary to make the statements therein not misleading.

          (xiv) Provide CUSIP numbers for all Transfer Restricted Securities not
     later than the effective date of the Shelf Registration Statement and
     provide the Trustee under the Indenture with certificates for the Notes
     that are in a form eligible for deposit with The Depository Trust Company.

          (xv) Cooperate and assist in any filings required to be made with the
     NASD and in the performance of any due diligence investigation by any
     underwriter that is required to be retained in accordance with the rules
     and regulations of the NASD.

          (xvi) Otherwise use its best efforts to comply with all applicable
     rules and regulations of the Commission and all reporting requirements
     under the rules and regulations of the Exchange Act.

          (xvii) Cause the Indenture to be qualified under the TIA not later
     than the effective date of the Shelf Registration Statement required by
     this Agreement, and, in connection therewith, cooperate with the trustee
     and the holders of Notes to effect such changes to the Indenture as may be
     required for such Indenture to be so qualified in accordance with the terms
     of the TIA; and execute and use its best efforts to cause the trustee
     thereunder to execute all documents that may be required to effect such
     changes and all other forms and documents required to be


                                       12
<PAGE>

     filed with the Commission to enable such Indenture to be so qualified in a
     timely manner.

          (xviii) Cause all Transfer Restricted Securities covered by the Shelf
     Registration Statement to be listed or quoted, as the case may be, on each
     securities exchange or automated quotation system on which similar
     securities issued by the Issuer are then listed or quoted.

          (xix) Provide promptly to each Holder upon written request each
     document filed with the Commission pursuant to the requirements of Section
     13 and Section 15 of the Exchange Act after the effective date of the Shelf
     Registration Statement.

          (xx) If requested by the underwriters, make appropriate officers of
     the Issuer available to the underwriters for meetings with prospective
     purchasers of the Transfer Restricted Securities and prepare and present to
     potential investors customary "road show" material in a manner consistent
     with new issuances of other securities similar to the Transfer Restricted
     Securities.

     (c) Each Holder agrees by acquisition of a Transfer Restricted Security
that, upon receipt of any notice from the Issuer of the existence of any fact of
the kind described in Section 4(b)(iii)(D) hereof, such Holder will, and will
use its reasonable best efforts to cause any underwriter(s) in an Underwritten
Offering to, forthwith discontinue disposition of Transfer Restricted Securities
pursuant to the Shelf Registration Statement until:

          (i) such Holder has received copies of the supplemented or amended
     Prospectus contemplated by Section 4(b)(xiii) hereof; or

          (ii) such Holder is advised in writing by the Issuer that the use of
     the Prospectus may be resumed, and has received copies of any additional or
     supplemental filings that are incorporated by reference in the Prospectus.

If so directed by the Issuer, each Holder will deliver to the Issuer (at the
Issuer's expense) all copies, other than permanent file copies then in such
Holder's possession, of the Prospectus covering such Transfer Restricted
Securities that was current at the time of receipt of such notice of suspension.

     (d) Each Holder who intends to be named as a selling Holder in the Shelf
Registration Statement shall furnish to the Issuer in writing, prior to or on
the 20th Business Day after receipt of a request therefor as set forth in a
questionnaire, such information regarding such Holder and the proposed
distribution by such Holder of its


                                       13
<PAGE>

Transfer Restricted Securities as the Issuer may reasonably request for use in
connection with the Shelf Registration Statement or Prospectus or preliminary
Prospectus included therein. (The form of the questionnaire is attached hereto
as Exhibit A.) Holders that do not complete the questionnaire and deliver it to
the Issuer shall not be named as selling securityholders in the Prospectus or
preliminary Prospectus included in the Shelf Registration Statement and
therefore shall not be permitted to sell any Transfer Restricted Securities
pursuant to the Shelf Registration Statement. Each Holder who intends to be
named as a selling Holder in the Shelf Registration Statement shall promptly
furnish to the Issuer in writing such other information as the Issuer may from
time to time reasonably request in writing. Each Holder as to which the Shelf
Registration Statement is being effected agrees to furnish promptly to the
Issuer all information required to be disclosed in order to make information
previously furnished to the Issuer by such Holder not materially misleading.

     (e) Upon the effectiveness of the Shelf Registration Statement, each Holder
shall notify the Issuer at least three Business Days prior to any intended
distribution of Transfer Restricted Securities pursuant to the Shelf
Registration Statement (a "Sale Notice"). Each Holder of this Security, by
accepting the same, agrees to hold any communication by the Issuer in response
to a Sale Notice in confidence.

     5. REGISTRATION EXPENSES.

     (a) All expenses incident to the Issuer's performance of or compliance with
this Agreement shall be borne by the Issuer regardless of whether a Shelf
Registration Statement becomes effective, including, without limitation:

          (i) all registration and filing fees and expenses (including filings
     made by any Initial Purchasers, Holders or underwriters with the NASD);

          (ii) all fees and expenses of compliance with federal securities and
     state Blue Sky or securities laws;

          (iii) all expenses of printing (including printing of Prospectuses and
     certificates for the Common Stock to be issued upon conversion of the
     Notes), messenger and delivery services and telephone;

          (iv) all fees and disbursements of counsel to the Issuer and, subject
     to Section 5(b) below, the Holders of Transfer Restricted Securities;

          (v) all application and filing fees in connection with listing (or
     authorizing for quotation) the Common Stock on a national securities
     exchange or automated quotation system pursuant to the requirements hereof;
     and


                                       14
<PAGE>

          (vi) all fees and disbursements of independent certified public
     accountants of the Issuer (including the expenses of any special audit and
     comfort letters required by or incident to such performance).

     The Issuer shall bear its internal expenses (including, without limitation,
all salaries and expenses of its officers and employees performing legal,
accounting or other duties), the expenses of any annual audit and the fees and
expenses of any Person, including special experts, retained by the Issuer.

     (b) In connection with the Shelf Registration Statement required by this
Agreement, the Issuer shall reimburse the Initial Purchasers and the Holders of
Transfer Restricted Securities being registered pursuant to the Shelf
Registration Statement, as applicable, for the reasonable fees and disbursements
of not more than one counsel, which shall be Debevoise & Plimpton, or such other
counsel as may be chosen by a Majority of Holders for whose benefit the Shelf
Registration Statement is being prepared.

     6. INDEMNIFICATION AND CONTRIBUTION.

     (a) The Issuer agrees to indemnify and hold harmless each Initial
Purchaser, each Holder and each Person who participates as an underwriter (any
such Person being an "Underwriter") and each Person, if any, who controls any
Initial Purchaser, Holder or Underwriter within the meaning of either Section 15
of the Securities Act or Section 20 of the Exchange Act as follows:

          (i) against any and all loss, liability, claim, damage and expense
     whatsoever, as incurred, arising out of any untrue statement or alleged
     untrue statement of a material fact contained in any Shelf Registration
     Statement (or any amendment thereto), including all documents incorporated
     therein by reference, or the omission or alleged omission therefrom of a
     material fact required to be stated therein or necessary to make the
     statements therein not misleading, or arising out of any untrue statement
     or alleged untrue statement of a material fact contained in any Prospectus
     (or any amendment or supplement thereto) or the omission or alleged
     omission therefrom of a material fact necessary in order to make the
     statements therein, in the light of the circumstances under which they were
     made, not misleading;

          (ii) against any and all loss, liability, claim, damage and expense
     whatsoever, as incurred, to the extent of the aggregate amount paid in
     settlement of any litigation, or any investigation or proceeding by any
     governmental agency or body, commenced or threatened, or of any claim
     whatsoever based upon any such untrue statement or


                                       15
<PAGE>

     omission, or any such alleged untrue statement or omission; PROVIDED that
     (subject to Section 6(d) below) any such settlement is effected with the
     written consent of the Issuer; and

          (iii) against any and all expense whatsoever, as incurred (including
     the fees and disbursements of counsel chosen by any indemnified party),
     reasonably incurred in investigating, preparing or defending against any
     litigation, or any investigation or proceeding by any governmental agency
     or body, commenced or threatened, or any claim whatsoever based upon any
     such untrue statement or omission, or any such alleged untrue statement or
     omission, to the extent that any such expense is not paid under
     subparagraph (i) or (ii) above;

PROVIDED, HOWEVER, that this indemnity agreement shall not apply to any loss,
liability, claim, damage or expense to the extent arising out of any untrue
statement or omission or alleged untrue statement or omission made in reliance
upon and in conformity with written information furnished to the Issuer by the
Initial Purchasers, such Holder or such Underwriter expressly for use in a Shelf
Registration Statement (or any amendment thereto) or any Prospectus (or any
amendment or supplement thereto).

     (b) Each Holder, severally but not jointly, agrees to indemnify and hold
harmless the Issuer, the Initial Purchasers, each Underwriter and the other
selling Holders and each Person, if any, who controls the Issuer, the Initial
Purchasers, any Underwriter or any other selling Holder within the meaning of
Section 15 of the Securities Act or Section 20 of the Exchange Act, against any
and all loss, liability, claim, damage and expense described in the indemnity
contained in Section 6(a) hereof, as incurred, but only with respect to untrue
statements or omissions, or alleged untrue statements or omissions, made in any
Shelf Registration Statement (or any amendment thereto) or any Prospectus (or
any amendment or supplement thereto) in reliance upon and in conformity with
written information with respect to such Holder furnished to the Issuer by such
Holder expressly for use in the Shelf Registration Statement (or any amendment
thereto) or such Prospectus (or any amendment or supplement thereto); PROVIDED,
HOWEVER, that no such Holder shall be liable for any claims hereunder in excess
of the amount of net proceeds received by such Holder from the sale of Transfer
Restricted Securities pursuant to such Shelf Registration Statement.

     (c) Each indemnified party shall give notice as promptly as reasonably
practicable to each indemnifying party of any action or proceeding commenced
against it in respect of which indemnity may be sought hereunder, but failure so
to notify an indemnifying party shall not relieve such indemnifying party from
any liability hereunder to the extent it is not materially prejudiced as a
result thereof and in any event shall not relieve it from any liability which it
may have otherwise than on account of this indemnity agreement. An indemnifying
party may participate at its own expense in the defense of such action;
PROVIDED, HOWEVER, that counsel to the indemnifying party shall not (except with
the


                                       16
<PAGE>

consent of the indemnified party) also be counsel to the indemnified party. In
no event shall the indemnifying party or parties be liable for the fees and
expenses of more than one counsel (in addition to any local counsel) separate
from their own counsel for all indemnified parties in connection with any one
action or separate but similar or related actions in the same jurisdiction
arising out of the same general allegations or circumstances. No indemnifying
party shall, without the prior written consent of the indemnified parties,
settle or compromise or consent to the entry of any judgment with respect to any
litigation, or any investigation or proceeding by any governmental agency or
body, commenced or threatened, or any claim whatsoever in respect of which
indemnification or contribution could be sought under this Section 6 (whether or
not the indemnified parties are actual or potential parties thereto), unless
such settlement, compromise or consent (i) includes an unconditional release of
each indemnified party from all liability arising out of such litigation,
investigation, proceeding or claim and (ii) does not include a statement as to
or an admission of fault, culpability or a failure to act by or on behalf of any
indemnified party.

     (d) If at any time an indemnified party shall have requested an
indemnifying party to reimburse the indemnified party for fees and expenses of
counsel, such indemnifying party agrees that it shall be liable for any
settlement of the nature contemplated by Section 6(a)(ii) effected without its
written consent if (i) such settlement is entered into more than 45 days after
receipt by such indemnifying party of the aforesaid request, (ii) such
indemnifying party shall have received notice of the terms of such settlement at
least 30 days prior to such settlement being entered into and (iii) such
indemnifying party shall not have reimbursed such indemnified party in
accordance with such request prior to the date of such settlement.

     (e) If the indemnification provided for in this Section 6 is for any reason
unavailable to or insufficient to hold harmless an indemnified party in respect
of any losses, liabilities, claims, damages or expenses referred to therein,
then each indemnifying party shall contribute to the aggregate amount of such
losses, liabilities, claims, damages and expenses incurred by such indemnified
party, as incurred, in such proportion as is appropriate to reflect the relative
fault of the indemnifying party or parties on the one hand and the indemnified
party or parties on the other hand in connection with the statements or
omissions which resulted in such losses, liabilities, claims, damages or
expenses, as well as any other relevant equitable considerations.

     The relative fault of the indemnifying party or parties on the one hand and
the indemnified party or parties on the other hand shall be determined by
reference to, among other things, whether any such untrue or alleged untrue
statement of a material fact or omission or alleged omission to state a material
fact relates to information supplied by the indemnifying party or parties on the
one hand or the indemnified party or parties on the


                                       17
<PAGE>

other hand and the parties' relative intent, knowledge, access to information
and opportunity to correct or prevent such statement or omission.

     The parties hereto agree that it would not be just and equitable if
contribution pursuant to this Section 6 were determined by pro rata allocation
or by any other method of allocation which does not take account of the
equitable considerations referred to above in this Section 6. The aggregate
amount of losses, liabilities, claims, damages and expenses incurred by an
indemnified party and referred to above in this Section 6 shall be deemed to
include any legal or other expenses reasonably incurred by such indemnified
party in investigating, preparing or defending against any litigation, or any
investigation or proceeding by any governmental agency or body, commenced or
threatened, or any claim whatsoever based upon any such untrue or alleged untrue
statement or omission or alleged omission.

     Notwithstanding the provisions of this Section 6, no Holder shall be
required to contribute any amount in excess of the amount by which the total
price at which the Transfer Restricted Securities purchased by it were resold
exceeds the amount of any damages which such Holder has otherwise been required
to pay by reason of any untrue or alleged untrue statement or omission or
alleged omission. The Holders' obligations to contribute as provided in this
Section 6(e) are several and not joint.

     No Person guilty of fraudulent misrepresentation (within the meaning of
Section 11(f) of the Securities Act) shall be entitled to contribution from any
Person who was not guilty of such fraudulent misrepresentation.

     For purposes of this Section 6, each Person, if any, who controls an
Initial Purchaser, a Holder or an Underwriter within the meaning of Section 15
of the Securities Act or Section 20 of the Exchange Act shall have the same
rights to contribution as such Initial Purchaser, such Holder or such
Underwriter, and each director of the Issuer, and each Person, if any, who
controls the Issuer within the meaning of Section 15 of the Securities Act or
Section 20 of the Exchange Act shall have the same rights to contribution as the
Issuer.


                                       18
<PAGE>

     7. RULE 144A. In the event the Issuer is not subject to Section 13 or 15(d)
of the Exchange Act, the Issuer hereby agrees with each Holder, for so long as
any Transfer Restricted Securities remain outstanding, to make available to any
Holder or beneficial owner of Transfer Restricted Securities in connection with
any sale thereof and any prospective purchaser of such Transfer Restricted
Securities from such Holder or beneficial owner, the information required by
Rule 144A(d)(4) under the Securities Act in order to permit resales of such
Transfer Restricted Securities pursuant to Rule 144A.

     8. PARTICIPATION IN UNDERWRITTEN REGISTRATIONS. No Holder may participate
in any Underwritten Registration hereunder unless such Holder:

          (i) agrees to sell such Holder's Transfer Restricted Securities on the
     basis provided in any underwriting arrangements approved by the Persons
     entitled hereunder to approve such arrangements and

          (ii) completes and executes all reasonable questionnaires, powers of
     attorney, indemnities, underwriting agreements, lock-up letters and other
     documents required under the terms of such underwriting arrangements.

     9. SELECTION OF UNDERWRITERS. The Holders of Transfer Restricted Securities
covered by the Shelf Registration Statement who desire to do so may sell such
Transfer Restricted Securities in an Underwritten Offering. In any such
Underwritten Offering, the investment banker or investment bankers and manager
or managers that will administer the offering will be selected by a Majority of
Holders whose Transfer Restricted Securities are included in such offering;
PROVIDED, that such investment bankers and managers must be reasonably
satisfactory to the Issuer.

     10. MISCELLANEOUS.

     (a) REMEDIES. The Issuer acknowledges and agrees that any failure by the
Issuer to comply with its obligations under Section 2 hereof may result in
material irreparable injury to the Initial Purchasers or the Holders for which
there is no adequate remedy at law, that it will not be possible to measure
damages for such injuries precisely and that, in the event of any such failure,
the Initial Purchasers or any Holder may obtain such relief as may be required
to specifically enforce the Issuer's obligations under Section 2 hereof. The
Issuer further agrees to waive the defense in any action for specific
performance that a remedy at law would be adequate.

     (b) ADJUSTMENTS AFFECTING TRANSFER RESTRICTED SECURITIES. The Issuer shall
not, directly or indirectly, take any action with respect to the Transfer
Restricted Securities as a class that would adversely affect the ability of the
Holders to include such Transfer Restricted Securities in a registration
undertaken pursuant to this Agreement.


                                       19
<PAGE>

     (c) NO INCONSISTENT AGREEMENTS. The Issuer will not, on or after the date
of this Agreement, enter into any agreement with respect to its securities that
is inconsistent with the rights granted to the Holders in this Agreement or
otherwise conflicts with the provisions hereof. In addition, the Issuer shall
not grant to any of its security holders (other than the holders of Transfer
Restricted Securities in such capacity) the right to include any of its
securities in the Shelf Registration Statement provided for in this Agreement
other than the Transfer Restricted Securities. The Issuer has not previously
entered into any agreement (which has not expired or been terminated) granting
any registration rights with respect to its securities to any Person which
rights conflict with the provisions hereof.

     (d) AMENDMENTS AND WAIVERS. This Agreement may not be amended, modified or
supplemented, and waivers or consents to or departures from the provisions
hereof may not be given, unless the Issuer has obtained the written consent of a
Majority of Holders.

     (e) NOTICES. All notices and other communications provided for or permitted
hereunder shall be made in writing by hand-delivery, first-class mail
(registered or certified, return receipt requested), telex, telecopier, or air
courier guaranteeing overnight delivery:

          (i) if to a Holder, at the address set forth on the records of the
     registrar under the Indenture or the transfer agent of the Common Stock, as
     the case may be; and

          (ii) if to the Issuer:

               Vertex Pharmaceuticals Incorporated
               130 Waverly Street
               Cambridge, Massachusetts 02139
               Attention:  Thomas G. Auchincloss, Jr., Vice President of Finance

               With a copy to:

               Kirkpatrick & Lockhart
               75 State Street
               Boston, Massachusetts 02109
               Attention: Eileen Smith Ewing, Esq.

     All such notices and communications shall be deemed to have been duly
given: at the time delivered by hand, if personally delivered; five Business
Days after being deposited in the mail, postage prepaid, if mailed; when
answered back, if telexed; when


                                       20
<PAGE>

receipt acknowledged, if telecopied; and on the next Business Day, if timely
delivered to an air courier guaranteeing overnight delivery.

     (f) SUCCESSORS AND ASSIGNS. This Agreement shall inure to the benefit of
and be binding upon the successors and assigns of each of the parties, including
without limitation and without the need for an express assignment, subsequent
Holders of Transfer Restricted Securities; PROVIDED, HOWEVER, that (i) this
Agreement shall not inure to the benefit of or be binding upon a successor or
assign of a Holder unless and to the extent such successor or assign acquired
Transfer Restricted Securities from such Holder and (ii) nothing contained
herein shall be deemed to permit any assignment, transfer or other disposition
of Transfer Restricted Securities in violation of the terms of the Purchase
Agreement or the Indenture. If any transferee of any Holder shall acquire
Transfer Restricted Securities, in any manner, whether by operation of law or
otherwise, such Transfer Restricted Securities shall be held subject to all of
the terms of this Agreement, and by taking and holding such Transfer Restricted
Securities such person shall be conclusively deemed to have agreed to be bound
by and to perform all of the terms and provisions of this Agreement.

     (g) COUNTERPARTS. This Agreement may be executed in any number of
counterparts and by the parties hereto in separate counterparts, each of which
when so executed shall be deemed to be an original and all of which taken
together shall constitute one and the same agreement.

     (h) SECURITIES HELD BY THE ISSUER OR ITS AFFILIATES. Whenever the consent
or approval of Holders of a specified percentage of Transfer Restricted
Securities is required hereunder, Transfer Restricted Securities held by the
Issuer or its "affiliates" (as such term is defined in Rule 405 under the
Securities Act) shall not be counted in determining whether such consent or
approval was given by the Holders of such required percentage.

     (i) HEADINGS. The headings in this Agreement are for convenience of
reference only and shall not limit or otherwise affect the meaning hereof.

     (j) GOVERNING LAW. This Agreement shall be governed by, and construed in
accordance with, the law of the State of New York, without regard to conflict of
laws principles thereof.

     (k) SEVERABILITY. If any one or more of the provisions contained herein, or
the application thereof in any circumstance, is held invalid, illegal or
unenforceable, the validity, legality and enforceability of any such provision
in every other respect and of the remaining provisions contained herein shall
not be affected or impaired thereby.


                                       21
<PAGE>

     (l) ENTIRE AGREEMENT. This Agreement is intended by the parties as a final
expression of their agreement and intended to be a complete and exclusive
statement of the agreement and understanding of the parties hereto in respect of
the subject matter contained herein. There are no restrictions, promises,
warranties or undertakings, other than those set forth or referred to herein
with respect to the registration rights granted by the Issuer with respect to
the Transfer Restricted Securities. This Agreement supersedes all prior
agreements and understandings between the parties with respect to such subject
matter


                                       22
<PAGE>

         IN WITNESS WHEREOF, the parties have executed this Agreement as of the
date first written above.

                            VERTEX PHARMECEUTICALS INCORPORATED

                            By
                               ------------------------------------------------
                               Name:
                               Title:

                            MERRILL LYNCH & CO.
                            MERRILL LYNCH, PIERCE, FENNER & SMITH
                                  INCORPORATED
                            BEAR, STEARNS & CO. INC.
                            CREDIT SUISSE FIRST BOSTON
                                  CORPORATION
                            FLEETBOSTON ROBERTSON STEPHENS INC.
                            SG COWEN SECURITIES CORPORATION,
                            as Representatives of the several Initial Purchasers

                            By: Merrill Lynch, Pierce, Fenner & Smith
                                        Incorporated

                            By:
                               ------------------------------------------------
                                          Authorized Signatory


<PAGE>

                                                            Exhibit A

                       VERTEX PHARMACEUTICALS INCORPORATED

             FORM OF SELLING SECURITYHOLDER NOTICE AND QUESTIONNAIRE

     The undersigned beneficial holder of 5% Convertible Subordinated Notes due
2007 (the "Notes") of Vertex Pharmaceuticals Incorporated (the "Issuer"), or
common stock, par value $.01 per share (the "Shares" and together with the
Notes, the "Transfer Restricted Securities"), of the Issuer understands that the
Issuer has filed, or intends to file, with the Securities and Exchange
Commission (the "Commission") a registration statement (the "Shelf Registration
Statement"), for the registration and resale under Rule 415 of the Securities
Act of 1933, as amended (the "Securities Act"), of the Transfer Restricted
Securities in accordance with the terms of the Registration Rights Agreement,
dated March 14, 2000 (the "Registration Rights Agreement"), between the Issuer
and Merrill Lynch & Co., Merrill Lynch, Pierce, Fenner & Smith Incorporated,
Bear, Stearns & Co. Inc., Credit Suisse First Boston Corporation, FleetBoston
Robertson Stephens Inc. and SG Cowen Securities Corporation, as Representatives
of the several Initial Purchasers. A copy of the Registration Rights Agreement
is available from the Issuer upon request at the address set forth below. All
capitalized terms not otherwise defined herein have the meaning ascribed thereto
in the Registration Rights Agreement.

     Each beneficial owner of Transfer Restricted Securities is entitled to the
benefits of the Registration Rights Agreement. In order to sell or otherwise
dispose of any Transfer Restricted Securities pursuant to the Shelf Registration
Statement, a beneficial owner of Transfer Restricted Securities generally will
be required to be named as a selling securityholder in the related Prospectus,
deliver a Prospectus to purchasers of Transfer Restricted Securities and be
bound by those provisions of the Registration Rights Agreement applicable to
such beneficial owner (including certain indemnification provisions, as
described below). BENEFICIAL OWNERS THAT DO NOT COMPLETE THIS NOTICE AND
QUESTIONNAIRE WITHIN 20 BUSINESS DAYS OF RECEIPT HEREOF AND DELIVER IT TO THE
ISSUER AS PROVIDED BELOW WILL NOT BE NAMED AS SELLING SECURITYHOLDERS IN THE
PROSPECTUS AND THEREFORE WILL NOT BE PERMITTED TO SELL ANY TRANSFER RESTRICTED
SECURITIES PURSUANT TO THE SHELF REGISTRATION STATEMENT.

     Certain legal consequences arise from being named as a selling
securityholder in the Shelf Registration Statement and the related Prospectus.
Accordingly, holders and beneficial owners of Transfer Restricted Securities are
advised to consult their own securities law counsel regarding the consequences
of being named or not being named as a selling securityholder in the Shelf
Registration Statement and the related Prospectus.


                                      A-1
<PAGE>

                                     NOTICE

     The undersigned beneficial owner (the "Selling Securityholder") of Transfer
Restricted Securities hereby gives notice to the Issuer of its intention to sell
or otherwise dispose of Transfer Restricted Securities beneficially owned by it
and listed below in Item 3 (unless otherwise specified under Item 3) pursuant to
the Shelf Registration Statement. The undersigned, by signing and returning this
Notice and Questionnaire, understands that it will be bound by the terms and
conditions of this Notice and Questionnaire and the Registration Rights
Agreement.

     Pursuant to the Registration Rights Agreement, the undersigned has agreed
to indemnify and hold harmless the Issuer, the Initial Purchasers, any
Underwriter and the other selling holders and each person, if any, who controls
such persons within the meaning of either Section 15 of the Securities Act or
Section 20 of the Exchange Act, from and against certain losses arising in
connection with statements concerning the undersigned made in the Shelf
Registration Statement or the related Prospectus in reliance upon the
information provided in this Notice and Questionnaire.

     The undersigned hereby provides the following information to the Issuer and
represents and warrants that such information is accurate and complete:

                                  QUESTIONNAIRE

1.   (a)  Full legal name of Selling Securityholder:

     (b)  Full legal name of registered holder (if not the same as (a) above)
          through which Transfer Restricted Securities listed in (3) below are
          held:

     (c)  Full legal name of DTC participant (if applicable and if not the same
          as (b) above) through which Transfer Restricted Securities listed in
          (3) are held:

2.   Address for notices to Selling Securityholders:

     Telephone:

     Fax:

     Contact Person:


                                      A-2
<PAGE>

3.   Beneficial ownership of Transfer Restricted Securities:

     (a)  Type of Transfer Restricted Securities beneficially owned, and
          principal amount of Notes or number of shares of Common Stock, as the
          case may be, beneficially owned:

     (b)  CUSIP No(s). of such Transfer Restricted Securities beneficially
          owned:

     4.   Beneficial ownership of the Issuer's securities owned by the Selling
          Securityholder:

          EXCEPT AS SET FORTH BELOW IN THIS ITEM (4), THE UNDERSIGNED IS NOT THE
          BENEFICIAL OR REGISTERED OWNER OF ANY SECURITIES OF THE ISSUER OTHER
          THAN THE TRANSFER RESTRICTED SECURITIES LISTED ABOVE IN ITEM (3)
          ("OTHER SECURITIES").

          (a)  Type and amount of Other Securities beneficially owned by the
               Selling Securityholder:

          (b)  CUSIP No(s). of such Other Securities beneficially owned:

     5.   Relationship with the Issuer

          Except as set forth below, neither the undersigned nor any of its
          affiliates, officers, directors or principal equity holders (5% or
          more) has held any position or office or has had any other material
          relationship with the Issuer (or their predecessors or affiliates)
          during the past three years.

          State any exceptions here:

     6.   Plan of Distribution

          Except as set forth below, the undersigned (including its donees or
          pledgees) intends to distribute the Transfer Restricted Securities
          listed above in Item (3) pursuant to the Shelf Registration Statement
          only as follows (if at all). Such Transfer Restricted Securities may
          be sold from time to time directly by the undersigned or,
          alternatively, through underwriters, broker-dealers or agents. If


                                      A-3
<PAGE>

          the Transfer Restricted Securities are sold through underwriters or
          broker-dealers, the Selling Securityholder will be responsible for
          underwriting discounts or commissions or agent's commissions. Such
          Transfer Restricted Securities may be sold in one or more transactions
          at fixed prices, at prevailing market prices at the time of sale, at
          varying prices determined at the time of sale, or at negotiated
          prices. Such sales may be effected in transactions (which may involve
          crosses or block transactions):

          (i)  on any national securities exchange or quotation service on which
               the Transfer Restricted Securities may be listed or quoted at the
               time of sale;

          (ii) in the over-the-counter market;

          (iii) in transactions otherwise than on such exchanges or services or
               in the over-the-counter market; or

          (iv) through the writing of options.

     In connection with sales of the Transfer Restricted Securities or
     otherwise, the undersigned may enter into hedging transactions with
     broker-dealers, which may in turn engage in short sales of the Transfer
     Restricted Securities and deliver Transfer Restricted Securities to close
     out such short positions, or loan or pledge Transfer Restricted Securities
     to broker-dealers that in turn may sell such securities.

     State any exceptions here:

     Note: In no event will such method(s) of distribution take the form of an
     underwritten offering of the Transfer Restricted Securities without the
     prior agreement of the Issuer.

          The undersigned acknowledges that it understands its obligation to
     comply with the provisions of the Exchange Act and the rules and
     regulations promulgated thereunder relating to stock manipulation,
     particularly Regulation M thereunder (or any successor rules or
     regulations), in connection with any offering of Transfer Restricted
     Securities pursuant to the Shelf Registration Statement. The undersigned
     agrees that neither it nor any person acting on its behalf will engage in
     any transaction in violation of such provisions.

          The Selling Securityholder hereby acknowledges its obligations under
     the Registration Rights Agreement to indemnify and hold harmless certain
     persons as set forth therein.


                                      A-4
<PAGE>

          Pursuant to the Registration Rights Agreement, the Issuer has agreed
     under certain circumstances to indemnify the Selling Securityholders
     against certain liabilities.

          In accordance with the undersigned's obligation under the Registration
     Rights Agreement to provide such information as may be required by law for
     inclusion in the Shelf Registration Statement, the undersigned agrees to
     promptly notify the Issuer of any inaccuracies or changes in the
     information provided herein that may occur subsequent to the date hereof at
     any time while the Shelf Registration Statement remains effective. All
     notices hereunder and pursuant to the Registration Rights Agreement shall
     be made in writing at the address set forth below.

          By signing below, the undersigned consents to the disclosure of the
     information contained herein in its answers to items (1) through (6) above
     and the inclusion of such information in the Shelf Registration Statement
     and the related Prospectus. The undersigned understands that such
     information will be relied upon by the Issuer in connection with the
     preparation or amendment of the Shelf Registration Statement and the
     related Prospectus.

          IN WITNESS WHEREOF, the undersigned, by authority duly given, has
     caused this Notice and Questionnaire to be executed and delivered either in
     person or by its duly authorized agent.

     Dated:

     Beneficial Owner

     By:
        -------------------------------
        Name:
        Title:

     Please return the completed and executed Notice and Questionnaire to Vertex
     Pharmaceuticals Incorporated at:

                         Vertex Pharmaceuticals Incorporated
                         130 Waverly Street
                         Cambridge, Massachusetts 02139
                         Attention:  Thomas G. Auchincloss, Jr.,
                                     Vice President of Finance


                                      A-5