Exhibit 99.4
                                                              Preliminary Copy

                         AURORA BIOSCIENCES CORPORATION

                    PROXY SOLICITED BY THE BOARD OF DIRECTORS
                      FOR A SPECIAL MEETING OF STOCKHOLDERS
                       TO BE HELD ON _______________, 2001

The undersigned appoints Stuart J.M. Collinson, Christopher W. Krueger and John
R. Pashkowsky, and each of them, as attorneys and proxies of the undersigned,
with full power of substitution, to vote all shares of stock of Aurora
Biosciences Corporation (the "Company") which the undersigned may be entitled to
vote at the Special Meeting of Stockholders of the Company to be held at the
___________ located at _________________________________ on ___________ at
___________ a.m., local time, and at any and all continuations, adjournments or
postponements thereof with all powers that the undersigned would possess if
personally present, upon and in respect of the following matters and in
accordance with the following instructions, with discretionary authority as to
any and all other matters that may properly come before the meeting.

         THIS PROXY, WHEN PROPERLY EXECUTED, WILL BE VOTED IN THE MANNER
DIRECTED HEREIN BY THE UNDERSIGNED STOCKHOLDER. UNLESS A CONTRARY DIRECTION IS
INDICATED, THIS PROXY WILL BE VOTED FOR PROPOSAL 1, AS MORE SPECIFICALLY
DESCRIBED IN THE JOINT PROXY STATEMENT-PROSPECTUS TRANSMITTED IN CONNECTION
WITH THE SPECIAL MEETING. ANY HOLDER WHO WISHES TO WITHHOLD THE DISCRETIONARY
AUTHORITY REFERRED TO IN PROPOSAL 2 BELOW SHOULD MARK A LINE THROUGH THE ENTIRE
PROPOSAL.

MANAGEMENT RECOMMENDS A VOTE FOR THE APPROVAL AND ADOPTION OF THE MERGER
AGREEMENT AND THE MERGER.

PROPOSAL 1  To approve and adopt the Agreement and Plan of Merger, dated April
            29, 2001, between Vertex Pharmaceuticals Incorporated ("Vertex"),
            Ahab Acquisition Sub, Inc. ("Merger Sub"), a wholly owned subsidiary
            of Vertex, and the Company, pursuant to which the Company will
            become a wholly-owned subsidiary of Vertex, and to approve the
            merger between the Company and Merger Sub.

         / / FOR                / / AGAINST            / / ABSTAIN

PROPOSAL 2  In their discretion, to transact any other business as may properly
            come before the special meeting or any adjournment or postponement
            of the special meeting.

Receipt of the Joint Proxy Statement -Prospectus dated ___________, 2001 is
hereby acknowledged.

Dated               , 2001
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                                               SIGNATURE(S)

                          PLEASE SIGN EXACTLY AS YOUR NAME APPEARS HEREON. IF
                          THE STOCK IS REGISTERED IN THE NAMES OF TWO OR MORE
                          PERSONS, EACH SHOULD SIGN. EXECUTORS, ADMINISTRATORS,
                          TRUSTEES, GUARDIANS AND ATTORNEYS-IN-FACT SHOULD ADD
                          THEIR TITLES. IF SIGNER IS A CORPORATION, PLEASE GIVE
                          FULL CORPORATE NAME AND HAVE A DULY AUTHORIZED OFFICER
                          SIGN, STATING TITLE. IF SIGNER IS A PARTNERSHIP,
                          PLEASE SIGN IN PARTNERSHIP NAME BY AN AUTHORIZED
                          PERSON.

PLEASE VOTE, DATE AND PROMPTLY RETURN THIS PROXY IN THE ENCLOSED RETURN ENVELOPE
WHICH IS POSTAGE PREPAID IF MAILED IN THE UNITED STATES.