<PAGE>

                                                                   EXHIBIT 10.20

THIS WARRANT AND THE SHARES OF CAPITAL STOCK ISSUED UPON ANY EXERCISE HEREOF
HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
"SECURITIES ACT"), OR ANY APPLICABLE STATE SECURITIES LAWS AND MAY NOT BE SOLD
OR OTHERWISE TRANSFERRED BY ANY PERSON, INCLUDING A PLEDGEE, UNLESS (1) EITHER
(A) A REGISTRATION WITH RESPECT TO THERETO SHALL BE EFFECTIVE UNDER THE
SECURITIES ACT, OR (B) THE COMPANY SHALL HAVE RECEIVED AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY THAT AN EXEMPTION FROM REGISTRATION UNDER THE
SECURITIES ACT IS AVAILABLE, AND (2) THERE SHALL HAVE BEEN COMPLIANCE WITH ALL
APPLICABLE STATE SECURITIES OR "BLUE SKY" LAWS.

No. W0001                                                       For the Purchase
                                                             of _________ shares
                                                                 of Common Stock


                            WARRANT TO PURCHASE STOCK

                                       OF

                                Variagenics, Inc.

                            (A DELAWARE CORPORATION)

         Variagenics, Inc., a Delaware corporation (the "Company"), for value
received, hereby certifies that Waters Investments Limited (the "Holder"), is
entitled, subject to the terms set forth below, to purchase from the Company, at
any time or from time to time on or after the date hereof and at or before the
earlier of 5:00 p.m. Eastern Standard time on the "Expiration Date" and the
termination of this Warrant as provided in Section 7 hereof, _____________
shares of Common Stock, par value $.01 per share, of the Company (the "Common
Stock"), at a purchase price per share equal to the "Base Price" subject to
adjustment of the Base Price upon the occurrence of certain events as set forth
in Section 3 of this Warrant. The "Expiration Date" shall be June___, 2005. The
"Base Price" shall initially be equal to the per share offering Price to Public
set forth on the cover page of the final Prospectus (as defined below). The
shares of stock issuable upon exercise of this Warrant, and the purchase price
per share, are hereinafter referred to as the "Warrant Stock" and the "Purchase
Price," respectively. On March 29, 2000, the Company filed with the United
States Securities and Exchange Commission ("SEC") a Registration Statement on
Form S-1 (No. 333-33558) ("Registration Statement") with respect to an initial
public offering of shares of its Common Stock. The term "Prospectus" as used
herein shall mean the prospectus, as amended, on file with the SEC at the time
the Registration Statement becomes effective, including the information deemed
to be part of the Registration Statement at the time of effectiveness pursuant
to Rule 430A, if applicable, except that if the prospectus filed by the Company
pursuant to Rule 424(b) differs from the prospectus on file at the time the
Registration
<PAGE>

Statement becomes effective, the term "Prospectus" shall refer to
the Rule 424(b) Prospectus from and after the time it was filed with the SEC or
transmitted to the SEC for filing.

         1.       EXERCISE.

                  1.1 MANNER OF EXERCISE; PAYMENT OF PURCHASE PRICE. This
         Warrant may be exercised by the Holder, in whole or in part, by
         surrendering this Warrant, with the purchase form appended hereto as
         EXHIBIT A duly executed by the Holder, at the principal office of the
         Company, or at such other place as the Company may designate,
         accompanied by payment in full of the Purchase Price payable in respect
         of the number of shares of Warrant Stock purchased upon such exercise.
         Payment of the Purchase Price shall be (i) in lawful money of the
         United States, in cash or by certified or official bank check payable
         to the order of the Company, in respect of the number of shares of
         Warrant Stock purchased upon such exercise or (ii) in accordance with
         subsection 1.4 below.

                  1.2 EFFECTIVENESS. Each exercise of this Warrant shall be
         deemed to have been effected immediately prior to the close of business
         on the day on which this Warrant shall have been surrendered to the
         Company as provided in Section 1.1 above. At such time, the person or
         persons in whose name or names any certificates for Warrant Stock shall
         be issuable upon such exercise as provided in Section 1.3 below shall
         be deemed to have become the holder or holders of record of the Warrant
         Stock represented by such certificates.

                  1.3. DELIVERY OF CERTIFICATES. As soon as practicable after
         the exercise of this Warrant in full or in part, and in any event
         within ten (10) business days thereafter, the Company at its sole
         expense will cause to be issued in the name of, and delivered to, the
         Holder, or, subject to the terms and conditions hereof, as such Holder
         (upon payment by such Holder of any applicable transfer taxes) may
         direct:

                           (a) A certificate or certificates for the number of
                  full shares of Warrant Stock to which such Holder shall be
                  entitled upon such exercise plus, in lieu of any fractional
                  share to which such Holder would otherwise be entitled, cash
                  in an amount determined pursuant to Section 2 hereof, and

                           (b) In case such exercise is in part only, a new
                  warrant or warrants (dated the date hereof) of like tenor,
                  calling in the aggregate on the face or faces thereof for the
                  number of shares of Warrant Stock (without giving effect to
                  any adjustment therein) equal to the number of such shares
                  called for on the face of this Warrant minus the number of
                  such shares purchased by the Holder upon such exercise as
                  provided in Section 1.1 above.

                  1.4 CASHLESS EXERCISE. The Holder may elect to receive,
         without the payment by the Holder of any additional consideration,
         shares equal to the value of this Warrant or any portion hereof then
         exercised by the surrender of this Warrant or such portion to the
         Company, with the net issue election notice appended hereto as EXHIBIT
         B duly executed,


                                       2

<PAGE>

         at the office of the Company. Thereupon, the Company shall issue to the
         Holder such number of fully paid and nonassessable shares of Common
         Stock as is computed using the following formula:

                                   X = Y (A-B)
                                       -------
                                          A
         where

                  X =    the number of shares to be issued to the Holder
                         pursuant to this subsection 1.4.

                  Y =    the number of shares covered by this Warrant in
                         respect of which the net issue election is made
                         pursuant to this subsection 1.4.

                  A =    the Fair Market Value of one share of Common Stock
                         (as defined in and determined in accordance with
                         Section 1.5 hereof) as at the time the net issue
                         election is made pursuant to this subsection 1.4.

                  B =    the Purchase Price in effect under this Warrant at
                         the time the net issue election is made pursuant to
                         this subsection 1.4.

                  1.5 FAIR MARKET VALUE OF COMMON STOCK. Fair Market Value of a
share of Common Stock means: (1) if the Common Stock is listed on a national
securities exchange or traded in the over-the-counter market and sales prices
are regularly reported for the Common Stock, the closing or last price of the
Common Stock on the Composite Tape or other comparable reporting system for the
trading day immediately preceding the applicable date; (2) if the Common Stock
is not traded on a national securities exchange but is traded on the
over-the-counter market, if sales prices are not regularly reported for the
Common Stock for the trading day referred to in clause (1), and if bid and asked
prices for the Common Stock are regularly reported, the mean between the bid and
the asked price for the Common Stock at the close of trading in the
over-the-counter market for the trading day on which Common Stock was traded
immediately preceding the applicable date; and (3) if the Common Stock is
neither listed on a national securities exchange nor traded in the
over-the-counter market, such value as reasonably determined in good faith by
the Board of Directors of the Company. The Board of Directors of the Company
shall promptly respond in writing to an inquiry by the Holder as to the Fair
Market Value of one share of Common Stock.

         2. FRACTIONAL SHARES. The Company shall not be required upon the
exercise of this Warrant to issue any fractional shares, but shall make an
adjustment therefor in cash on the basis of the Fair Market Value of the Warrant
Stock as determined pursuant to Section 1.5 hereof.


                                       3
<PAGE>

         3.       ADJUSTMENTS.

                  3.1. CHANGES IN COMMON STOCK. If the Company shall (i) combine
         the outstanding shares of Common Stock into a lesser number of shares,
         (ii) subdivide the outstanding shares of Common Stock into a greater
         number of shares, or (iii) issue additional shares of Common Stock as a
         dividend or other distribution with respect to the Common Stock, the
         number of shares of Warrant Stock shall be equal to the number of
         shares which the Holder would have been entitled to receive after the
         happening of any of the events described above if such shares had been
         issued immediately prior to the happening of such event, such
         adjustment to become effective concurrently with the effectiveness of
         such event. The Purchase Price in effect immediately prior to any such
         combination of Common Stock shall, upon the effectiveness of such
         combination, be proportionately increased. The Purchase Price in effect
         immediately prior to any such subdivision of Common Stock or at the
         record date of such dividend shall upon the effectiveness of such
         subdivision or immediately after the record date of such dividend be
         proportionately reduced.

                  3.2 REORGANIZATIONS AND RECLASSIFICATIONS. If there shall
         occur any capital reorganization or reclassification of the Common
         Stock (other than a change in par value or a subdivision or combination
         as provided for in Section 3.1), then, as part of any such
         reorganization or reclassification, lawful provision shall be made so
         that the Holder shall have the right thereafter to receive upon the
         exercise hereof the kind and amount of shares of stock or other
         securities or property which such Holder would have been entitled to
         receive if, immediately prior to any such reorganization or
         reclassification, such Holder had held the number of shares of Common
         Stock which were then purchasable upon the exercise of this Warrant. In
         any such case, appropriate adjustment (as reasonably determined by the
         Board of Directors of the Company) shall be made in the application of
         the provisions set forth herein with respect to the rights and
         interests thereafter of the Holder such that the provisions set forth
         in this Section 3 (including provisions with respect to adjustment of
         the Purchase Price) shall thereafter be applicable, as nearly as is
         reasonably practicable, in relation to any shares of stock or other
         securities or property thereafter deliverable upon the exercise of this
         Warrant.

                  3.3      [INTENTIONALLY OMITTED.]

                  3.4 CERTIFICATE OF ADJUSTMENT. When any adjustment is required
         to be made in the Purchase Price, the Company shall promptly mail to
         the Holder a certificate setting forth the Purchase Price after such
         adjustment and setting forth a brief statement of the facts requiring
         such adjustment. Delivery of such certificate shall be deemed to be a
         final and binding determination with respect to such adjustment unless
         challenged by the Holder within ten (10) days of receipt thereof. Such
         certificate shall also set forth the kind and amount of stock or other
         securities or property into which this Warrant shall be exercisable
         following the occurrence of any of the events specified in this Section
         3.


                                       4
<PAGE>

         4.       COMPLIANCE WITH SECURITIES ACT.

                  4.1 UNREGISTERED SECURITIES. The Holder acknowledges that this
         Warrant and the Warrant Stock have not been registered under the
         Securities Act of 1933, as amended, and the rules and regulations
         thereunder, or any successor legislation (the "Securities Act"), and
         agrees not to sell, pledge, distribute, offer for sale, transfer or
         otherwise dispose of this Warrant or any Warrant Stock in the absence
         of (i) an effective registration statement under the Securities Act
         covering this Warrant or such Warrant Stock and registration or
         qualification of this Warrant or such Warrant Stock under any
         applicable "blue sky" or state securities law then in effect, or (ii)
         an opinion of counsel, satisfactory to the Company, that such
         registration and qualification are not required. The Company may delay
         issuance of the Warrant Stock until completion of any action or
         obtaining of any consent, which the Company deems necessary under any
         applicable law (including without limitation state securities or "blue
         sky" laws).

                  4.2 INVESTMENT LETTER. Without limiting the generality of
         Section 4.1, unless the offer and sale of any shares of Warrant Stock
         shall have been effectively registered under the Securities Act, the
         Company shall be under no obligation to issue the Warrant Stock unless
         and until the Holder shall have executed an investment letter in form
         and substance satisfactory to the Company, including a warranty at the
         time of such exercise that the Holder is acquiring such shares for its
         own account, for investment and not with a view to, or for sale in
         connection with, the distribution of any such shares.

                  4.3 LEGEND. Certificates delivered to the Holder pursuant to
         Section 1.3 shall bear the following legend or a legend in
         substantially similar form:

                  "THE SHARES REPRESENTED BY THIS CERTIFICATE HAVE BEEN TAKEN
                  FOR INVESTMENT AND THEY MAY NOT BE SOLD OR OTHERWISE
                  TRANSFERRED BY ANY PERSON, INCLUDING A PLEDGEE, IN THE ABSENCE
                  OF AN EFFECTIVE REGISTRATION STATEMENT FOR THE SHARES UNDER
                  THE SECURITIES ACT OF 1933, AS AMENDED, OR AN OPINION OF
                  COUNSEL, SATISFACTORY TO THE COMPANY, THAT AN EXEMPTION FROM
                  REGISTRATION IS THEN AVAILABLE."

         5. RESERVATION OF STOCK. The Company will at all times reserve and keep
available, solely for issuance and delivery upon the exercise of this Warrant,
such shares of Warrant Stock and other stock, securities and property, as from
time to time shall be issuable upon the exercise of this Warrant. The Company
covenants that all shares of Warrant Stock so issuable will, when issued, be
duly and validly issued and fully paid and nonassessable.

         6. REPLACEMENT OF WARRANTS. Upon receipt of evidence reasonably
satisfactory to the Company of the loss, theft, destruction or mutilation of
this Warrant and (in the case of loss, theft or destruction) upon delivery of an
indemnity agreement (with surety if reasonably required) in an amount reasonably
satisfactory to the Company, or (in the case of mutilation) upon surrender and
cancellation of this Warrant, the Company will issue, in lieu thereof, a new
Warrant of like tenor.


                                       5
<PAGE>

         7. TERMINATION UPON CERTAIN EVENTS. In the event of a sale of all or
substantially all of the assets of the Company to, or a merger or consolidation
of the Company with or into, any other entity (other than (i) a merger in which
the sole consideration delivered to the stockholders of the Company consists of
equity securities of the surviving corporation, or (ii) a merger the sole
purpose of which is to change the state of incorporation of the Company) or a
dissolution or the adoption of a plan of liquidation of the Company, the Company
shall give the Holder notice of any such sale, merger, consolidation,
dissolution or adoption at least 30 days prior to the effective date of such
sale, merger, consolidation, dissolution or adoption (the "Effective Date"). If
this Warrant shall not have otherwise terminated or expired, the Holder shall
have the right until 5:00 p.m, Eastern Standard Time, on the day immediately
prior to the Effective Date to exercise its rights hereunder to the extent not
previously exercised, but may make such exercise conditional upon the
consummation of any such transaction on the Effective Date. In the event that
the Holder does not exercise or give notice to the Company of its intent not to
exercise its rights hereunder prior to the Effective Date, the Holder shall be
deemed to have exercised its right to exercise this Warrant pursuant to Section
1.4 hereof and shall be treated as if Holder had exercised this Warrant under
such Section 1.4 at the close of business on the day immediately prior to the
Effective Date, and upon the delivery of the cash or other property due to the
Holder under Section 1.4 hereof, this Warrant shall terminate.

         8. TRANSFERABILITY. Without the prior written consent of the Company,
the Warrant shall not be assigned, pledged or hypothecated in any way (whether
by operation of law or otherwise) and shall not be subject to execution,
attachment or similar process; PROVIDED, HOWEVER, that this Warrant may be
transferred without consent to any 100% Affiliate of the Holder. Any attempted
transfer, assignment, pledge, hypothecation or other disposition of the Warrant
or of any rights granted hereunder contrary to the provisions of this Section 8,
or the levy of any attachment or similar process upon the Warrant or such
rights, shall be null and void. For the purposes of this Section 8, "100%
Affiliate" shall mean any company, corporation, business or entity controlled
by, controlling, or under common control with either party to this Agreement.
For this purpose, "control" means direct or indirect beneficial ownership of a
one hundred percent (100%) interest in the voting stock (or the equivalent) of
such corporation or other business.

         9. NO RIGHTS AS STOCKHOLDER. Until the exercise of this Warrant, the
Holder shall not have or exercise any rights by virtue hereof as a stockholder
of the Company.

         10. LOCK-UP AGREEMENT. If, in connection with a registration statement
filed by the Company pursuant to the Securities Act with respect to an
underwritten public offering, the Company or its underwriter so requests, Holder
agrees not to sell or otherwise transfer or dispose of any of the Warrant Stock
for a period not to exceed one hundred and eighty (180) days following the
effectiveness of such registration, and to enter into an agreement to such
effect; PROVIDED that all of (i) the Company's directors and officers, (ii) the
holders of at least 2% of the outstanding Common Stock (or securities
convertible into at least 2% of the Common Stock), and (iii) the other holders
of securities of the Company participating in the underwriting enter into
similar agreements. The Company may impose stop-transfer instructions with
respect to the Shares subject to the foregoing restriction until the end of said
period.


                                       6
<PAGE>

         11. NOTICES. All notices, requests and other communications hereunder
shall be in writing, shall be either (i) delivered by hand, (ii) made by,
telecopy or facsimile transmission, (iii) sent by overnight courier, or (iv)
sent by registered mail, postage prepaid, return receipt requested. In the case
of notices from the Company to the Holder, they shall be sent to the address
furnished to the Company in writing by the last Holder who shall have furnished
an address to the Company in writing. All notices from the Holder to the Company
shall be delivered to the Company at its principal offices or such other address
as the Company shall so notify the Holder. All notices, requests and other
communications hereunder shall be deemed to have been given (i) by hand, at the
time of the delivery thereof to the receiving party at the address of such party
described above, (ii) if made by telecopy or facsimile transmission, at the time
that receipt thereof has been acknowledged by electronic confirmation or
otherwise, (iii) if sent by overnight courier, on the next business day
following the day such notices is delivered to the courier service, or (iv) if
sent by registered mail, on the fifth business day following the day such
mailing is made.

         12. WAIVERS AND MODIFICATIONS. Any term or provision of this Warrant
may be waived only by written document executed by the party entitled to the
benefits of such terms or provisions. The terms and provisions of this Warrant
may be modified or amended only by written agreement executed by the parties
hereto.

         13. HEADINGS. The headings in this Warrant are for convenience of
reference only and shall in no way modify or affect the meaning or construction
of any of the terms or provisions of this Warrant.

         14. GOVERNING LAW. This Warrant will be governed by and construed in
accordance with and governed by the law of the Commonwealth of Massachusetts,
without giving effect to the conflict of law principles thereof.


                                       7
<PAGE>

                                       Variagenics, Inc.


                                       By:________________________________
                                       Name:    Taylor J. Crouch
                                       Title:   President


[Corporate Seal]
ATTEST:

----------------------------


                                       8
<PAGE>

                                    EXHIBIT A

                                  PURCHASE FORM

To:      Variagenics, Inc.

         The undersigned pursuant to the provisions set forth in the attached
Warrant (No. W-0001), hereby irrevocably elects to purchase ______ shares of the
Common Stock, par value $.01 per share (the "Common Stock") of Variagenics,
Inc., covered by such Warrant and herewith makes payment of $__________,
representing the full purchase price for such shares at the price per share
provided for in such Warrant. The Common Stock for which the Warrant may be
exercised shall be known herein as the "Warrant Stock".

         The undersigned is aware that the Warrant Stock has not been and will
not be registered under the Securities Act of 1933, as amended (the "Securities
Act") or any state securities laws. The undersigned understands that reliance by
the Company on exemptions under the Securities Act is predicated in part upon
the truth and accuracy of the statements of the undersigned in this Purchase
Form.

         The undersigned represents and warrants that (1) it has been furnished
with all information which it deems necessary to evaluate the merits and risks
of the purchase of the Warrant Stock, (2) it has had the opportunity to ask
questions concerning the Warrant Stock and the Company and all questions posed
have been answered to its satisfaction, (3) it has been given the opportunity to
obtain any additional information it deems necessary to verify the accuracy of
any information obtained concerning the Warrant Stock and the Company and (4) it
has such knowledge and experience in financial and business matters that it is
able to evaluate the merits and risks of purchasing the Warrant Stock and to
make an informed investment decision relating thereto.

         The undersigned hereby represents and warrant that it is purchasing the
Warrant Stock for its own account for investment and not with a view to the sale
or distribution of all or any part of the Warrant Stock.

         The undersigned understands that because the Warrant Stock has not been
registered under the Securities Act, it must continue to bear the economic risk
of the investment for an indefinite period of time and the Warrant Stock cannot
be sold unless it is subsequently registered under applicable federal and state
securities laws or an exemption from such registration is available.

         The undersigned agrees that it will in no event sell or distribute or
otherwise dispose of all or any part of the Warrant Stock unless (1) there is an
effective registration statement under the Securities Act and applicable state
securities laws covering any such transaction involving the Warrant Stock, or
(2) the Company receives an opinion satisfactory to the Company of the
undersigned's legal counsel stating that such transaction is exempt from
registration. The


                                       9
<PAGE>

undersigned consents to the placing of a legend on its certificate for the
Warrant Stock stating that the Warrant Stock has not been registered and setting
forth the restriction on transfer contemplated hereby and to the placing of a
stop transfer order on the books of the Company and with any transfer agents
against the Warrant Stock until the Warrant Stock may be legally resold or
distributed without restriction.

         The undersigned has considered the federal and state income tax
implications of the exercise of the Warrant and the purchase and subsequent sale
of the Warrant Stock.



                                         ______________________________________

                                         Dated: _______________________________


                                       10
<PAGE>

                                                                       EXHIBIT B

                            NET ISSUE ELECTION NOTICE


To:      Variagenics, Inc.                            Dated:  __________________

         The undersigned hereby elects to exercise Warrant No. 0001 for ___
shares of Common Stock and hereby elects under Subsection 1.4 to surrender the
right to purchase _________ shares of Common Stock pursuant to said Warrant. The
certificate(s) for the shares issuable upon such net issue election shall be
issued in the name of the undersigned or as otherwise indicated below.

         The undersigned is aware that the Warrant Stock has not been and will
not be registered under the Securities Act of 1933, as amended (the "Securities
Act") or any state securities laws. The undersigned understands that reliance by
the Company on exemptions under the Securities Act is predicated in part upon
the truth and accuracy of the statements of the undersigned in this Purchase
Form.

         The undersigned represents and warrants that (1) it has been furnished
with all information which it deems necessary to evaluate the merits and risks
of the purchase of the Warrant Stock, (2) it has had the opportunity to ask
questions concerning the Warrant Stock and the Company and all questions posed
have been answered to its satisfaction, (3) it has been given the opportunity to
obtain any additional information it deems necessary to verify the accuracy of
any information obtained concerning the Warrant Stock and the Company and (4) it
has such knowledge and experience in financial and business matters that it is
able to evaluate the merits and risks of purchasing the Warrant Stock and to
make an informed investment decision relating thereto.

         The undersigned hereby represents and warrant that it is purchasing the
Warrant Stock for its own account for investment and not with a view to the sale
or distribution of all or any part of the Warrant Stock.

         The undersigned understands that because the Warrant Stock has not been
registered under the Securities Act, it must continue to bear the economic risk
of the investment for an indefinite period of time and the Warrant Stock cannot
be sold unless it is subsequently registered under applicable federal and state
securities laws or an exemption from such registration is available.


                                       11
<PAGE>

         The undersigned agrees that it will in no event sell or distribute or
otherwise dispose of all or any part of the Warrant Stock unless (1) there is an
effective registration statement under the Securities Act and applicable state
securities laws covering any such transaction involving the Warrant Stock, or
(2) the Company receives an opinion satisfactory to the Company of the
undersigned's legal counsel stating that such transaction is exempt from
registration. The undersigned consents to the placing of a legend on its
certificate for the Warrant Stock stating that the Warrant Stock has not been
registered and setting forth the restriction on transfer contemplated hereby and
to the placing of a stop transfer order on the books of the Company and with any
transfer agents against the Warrant Stock until the Warrant Stock may be legally
resold or distributed without restriction.

         The undersigned has considered the federal and state income tax
implications of the exercise of the Warrant and the purchase and subsequent sale
of the Warrant Stock.



                                      _______________________________________
                                      Signature


                                      _______________________________________
                                      Name for Registration


                                      _______________________________________
                                      Mailing Address


                                       12