PRELIMINARY COPY                                                   EXHIBIT 99.3

                       VERTEX PHARMACEUTICALS INCORPORATED

            SPECIAL MEETING OF STOCKHOLDERS - __________ _____, 2001

           THIS PROXY IS SOLICITED ON BEHALF OF THE BOARD OF DIRECTORS

         The undersigned does hereby constitute and appoint Joshua S. Boger and
Vicki L. Sato, or either one of them, the attorney(s) of the undersigned, with
full power of substitution, with all the powers which the undersigned would
possess if personally present, to vote all stock of Vertex Pharmaceuticals
Incorporated which the undersigned is entitled to vote at the Special Meeting of
Stockholders of Vertex Pharmaceuticals Incorporated to be held at 130 Waverly
Street, Cambridge, Massachusetts, on ___________, __________ _____, 2001 at
__________ A.M. Eastern Time and at any adjournments thereof, hereby
acknowledging receipt of the Proxy Statement for such meeting and revoking all
previous proxies.

         This Proxy, when properly executed, will be voted as directed. IF NO
DIRECTION IS MADE, THIS PROXY WILL BE VOTED FOR THE PROPOSALS LISTED ON THE
REVERSE SIDE AND, IN THE CASE OF OTHER MATTERS THAT LEGALLY COME BEFORE THE
MEETING, AS SAID ATTORNEY(S) MAY DEEM ADVISABLE.

                  (Continued and to be signed on reverse side)
                                                                SEE REVERSE SIDE





PLEASE VOTE, SIGN, DATE, AND RETURN THE PROXY CARD PROMPTLY USING THE ENCLOSED
ENVELOPE.

1. Approval of the issuance of shares of Vertex common stock in connection with
the merger between Vertex and Aurora Biosciences Corporation as described in the
accompanying joint proxy statement-prospectus.

[__] For    [__] Against    [__] Abstain

2. Approval of the amendment to the 1996 Stock and Option Plan to increase the
number of shares of common stock reserved for issuance under the plan from
13,000,000 to 16,000,000.

[__] For    [__] Against    [__] Abstain

In accordance with their judgment, the proxies are authorized to vote upon such
other matters as may properly come before the Special Meeting or any
postponement or adjournment thereof.

Mark here for address                       Mark here if you plan
change and note at left  [__]               to attend the  meeting  [__]

                                            Please sign name exactly as name
                                            appears. When signing in a fiduciary
                                            capacity, please give full title.
                                            Co-fiduciaries and joint owners
                                            should each sign.

Signature: _____________ Date: ________ Signature: ______________ Date: ________