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                                                                   Exhibit 10.21



                                VARIAGENICS, INC.
                               60 HAMPSHIRE STREET
                               CAMBRIDGE, MA 02139

                                                                   June 21, 2000

Waters Investments Limited
109 Lukens Drive
New Castle, DE 19720

                         Re: COMMON STOCK PURCHASE AGREEMENT

Ladies and Gentlemen:

         WHEREAS, Variagenics, Inc., a Delaware corporation (the "Company") and
Waters Technologies Corporation, a Delaware corporation ("Waters") have entered
into a Strategic Alliance Agreement dated as of the date hereof (the "Alliance
Agreement");

         WHEREAS, in connection with the Alliance Agreement, the Company and
Waters Investments Limited (the "Purchaser"), an affiliate of Waters, desire to
enter into this Common Stock Purchase Agreement (the "Purchase Agreement") and a
Standstill Agreement of even date herewith (the "Standstill Agreement") and that
the Purchaser shall sign a Lock-Up Letter in the form attached hereto as EXHIBIT
A; and

         WHEREAS, (i) 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 "Company IPO"), (ii) the
Purchaser acknowledges that it has received a copy of the Registration Statement
and that it has access to the Registration Statement, with exhibits, over the
Internet, and that it has had access to such officers of, and information from,
the Company as it deems prudent and (iii) the Company has advised Purchaser that
the Company IPO is contemplated to be underwritten by Credit Suisse First Boston
Corporation as managing underwriter and Chase Securities Inc. and SG Cowen
Securities Corporation as co-underwriters (collectively, the "Underwriters").

         NOW, THEREFORE, in consideration for the premises and mutual covenants
contained in this Purchase Agreement, the Alliance Agreement and the Standstill
Agreement, and for other good and valuable consideration, the receipt and
sufficiency of which is hereby acknowledged, the parties hereto agree as
follows:


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         SECTION 1. PURCHASE OF SHARES.

         1.1 Subject to the provisions of Section 4.3 hereof, in the event that
the IPO Closing (as defined below) shall take place on or before August 31,
2000, contemporaneously with such IPO Closing, Purchaser shall purchase and the
Company shall issue and sell to Purchaser at the Per-Share Purchase Price (as
defined below) such number of shares of the Common Stock of the Company, par
value $.01 per share (the "Purchased Common Shares") as shall equal, to the
nearest whole number, the quotient of $7,500,000 divided by the per share
offering Price to Public set forth on the cover page of the final Prospectus, as
defined below (the "Per-Share Purchase Price") at a closing to take place at the
offices of Mintz, Levin, Cohn, Ferris, Glovsky and Popeo, P.C. Upon the date of
such closing, the Company shall deliver to Purchaser one or more stock
certificates, pursuant to the Purchaser's reasonable request, representing the
Purchased Common Shares. Each such certificate shall be registered in the name
of the Purchaser. The Company's obligation to issue and deliver the Purchased
Common Shares shall be subject to the following conditions, any of which may be
waived by the Company: (a) receipt by the Company of a certified or official
bank check or checks or wire transfer of funds in the full amount of the
purchase price for the Purchased Common Shares; and (b) the accuracy of the
representations and warranties made by the Purchaser herein as though such
representations and warranties had been made on and as of Closing. 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 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. The "IPO
Closing" as used herein shall mean the first date upon which the Company
receives from the Underwriters the proceeds of the Company IPO, less
underwriting discount and commissions.

         1.2 Subject to the provisions of Section 4.3 hereof, in the event that
that Closing of the Company IPO does not take place on or before August 31,
2000, then the Company will issue and sell to Purchaser and Purchaser will buy
from the Company, ______________ shares [to be calculated based upon a $200
million pre-money company valuation] (the "Alternate Common Shares") of the
Company's Common Stock for an aggregate purchase price of $7,500,000.00 at a
closing to take place at the offices of Mintz, Levin, Cohn, Ferris, Glovsky and
Popeo, P.C. at 10:00 a.m. on [September 11, 2000], or at such time and date
thereafter as the Purchaser and the Company shall mutually agree. Upon the date
of such closing, the Company shall deliver to Purchaser one or more stock
certificates, pursuant to the Purchaser's reasonable request, representing the
Alternate Common Shares. Each such certificate shall be registered in the name
of the Purchaser. The Company's obligation to issue and deliver the Purchased
Common Shares shall be subject to the following conditions, any of which may be
waived by the Company: (a) receipt by the Company of a certified or official
bank check or checks or wire transfer of funds in the full amount of the
purchase price for the Purchased Common Shares; and (b) the accuracy of the
representations and warranties made by the Purchaser herein as though such
representations and warranties had been made on and as of such closing.


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         1.3 The Purchased Common Shares and the Alternate Common Shares may
hereinafter be referred to as the "Shares."

         SECTION 2. COMPANY REPRESENTATIONS AND WARRANTIES.

         The Company hereby represents and warrants to Purchaser as follows:

         2.1 The Company is a corporation duly organized, validly existing and
in good standing under the laws of the State of Delaware. The Company has full
power and authority to own and operate its properties and assets, and to carry
on its business as presently conducted. The Company is duly qualified, is
authorized to do business and is in good standing as a foreign corporation in
all jurisdictions in which the nature of its activities and of its properties
(both owned and leased) makes such qualification necessary, except for those
jurisdictions, in the aggregate, in which failure to do so would not have a
material adverse effect on the Company or its business.

         2.2 All corporate action on the part of the Company, its officers,
directors and shareholders necessary for the authorization, execution and
delivery of this Purchase Agreement, for the sale and issuance of the Shares
pursuant hereto and for the performance of the Company's obligations hereunder
has been taken or will be taken prior to any closing contemplated hereunder.
This Agreement, when executed and delivered, will be a valid and binding
obligation of the Company enforceable in accordance with its terms. The sale of
the Shares is not and will not be subject to any preemptive rights or rights of
first refusal that have not been properly waived or complied with.

         2.3 The execution, delivery and performance of and compliance with this
Purchase Agreement and the issuance and sale of the Shares pursuant hereto will
not (i) materially conflict with, or result in a material breach or violation
of, or constitute a material default under, or result in the creation or
imposition of any material lien under, any statute, law, rule or regulation,
judgment, order or decree applicable to the Company, (ii) violate, conflict with
or result in the breach of any material terms of, or result in the material
modification of, or create a material lien under, any material contract or
otherwise give any other contracting party the right to terminate a material
contract, or constitute (or with notice or lapse of time both constitute) a
material default under any material contract to which the Company is a party or
by or to which it or any of its assets or properties may be bound or subject or
(iii) result in any violation, or be in conflict with or constitute a default
under any term, of its Certificate of Incorporation or bylaws.

         2.4 The Shares which will be purchased by Purchaser hereunder, when
issued, sold and delivered in accordance with the terms hereof for the
consideration expressed herein, will be duly and validly authorized and issued,
fully paid and nonassessable, and will be free of any liens or encumbrances.

         2.5 There is no action, suit, proceeding nor, to the Company's
knowledge, any investigation pending or currently threatened against the
Company, that questions the validity of this Purchase Agreement or the right of
the Company to enter into this Purchase Agreement.


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         2.6 No consent, approval or authorization of, or designation,
declaration or filing with, any governmental authority on the part of the
Company is required in connection with the valid execution, delivery, and
performance of this Agreement or the offer, sale or issuance of the Shares, or
the consummation of any other transaction contemplated by this Purchase
Agreement except certain filings as may be required under the Securities Act and
state securities laws and regulations, which filings will be made timely in
accordance with the applicable law or regulation.

         2.7 The Company has delivered to Purchaser a true and complete copy of
the Registration Statement. Such Registration Statement complies as to form in
all material respects with the rules and regulations of the SEC applicable to
the Registration Statement. Such Registration Statement does not, and any
amendments thereto will not, contain at the time of filing any untrue statement
of a material fact or omit to state a material fact required to be stated
therein.

         SECTION 3. REPRESENTATIONS AND WARRANTIES OF THE PURCHASER

         Purchaser hereby represents to the Company as follows:

         3.1 Purchaser is an "accredited investor" as such term is defined in
Rule 501 of Regulation D under the Securities Act and is a sophisticated
investor and has such knowledge and experience in financial, tax, business
matters, securities and investments including, without limitation, experience in
investments such as the purchase of the Shares, as to enable Purchaser to
utilize the information made available to it in connection with the sale of the
Shares, to evaluate the merits and risks of an investment in the Shares and to
make an informed investment decision with respect thereto;

         3.2 Prior to the execution of this Purchase Agreement, the Purchaser
has received a copy of the Registration Statement and has had the opportunity to
ask questions of and receive answers from representatives of the Company
concerning the finances, operations, business and prospects of the Company.

         3.3 Purchaser understands that the Shares are not being registered
under the Securities Act of 1933, as amended (the "Securities Act"), and are not
being registered under any state "blue sky" securities laws, and the Shares may
not be transferred except in compliance with such laws;

         3.4 Purchaser is acquiring the Shares solely for its own account for
investment and not with a view to, or for resale in connection with, any
distribution thereof and has no present intention of transferring, distributing
or selling the Shares to any other person or entity;

         3.5 Purchaser understands that it must bear the economic risk of the
investment indefinitely because none of the Shares have been registered under
applicable securities laws and therefore, none of the Shares may be sold,
hypothecated or otherwise disposed of unless subsequently registered under the
Securities Act and applicable state securities laws or an


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exemption from registration is available and, accordingly, that a legend shall
be placed on the certificate(s) representing the Shares in substantially the
following 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, UNLESS (1) EITHER (A) A REGISTRATION
         STATEMENT WITH RESPECT TO SUCH SHARES SHALL BE EFFECTIVE UNDER THE
         SECURITIES ACT OF 1933, AS AMENDED, OR (B) THE COMPANY SHALL HAVE
         RECEIVED AN OPINION OF COUNSEL SATISFACTORY TO IT THAT AN EXEMPTION
         FROM REGISTRATION UNDER SUCH ACT IS THEN AVAILABLE, AND (2) THERE SHALL
         HAVE BEEN COMPLIANCE WITH ALL APPLICABLE STATE SECURITIES LAWS."

         3.6 The representations of Purchaser contained herein are accurate and
may be relied upon by the Company in determining the availability of an
exemption from registration under the Securities Act and state securities laws
in connection with the offering and sale of the Shares;

         3.7 Purchaser has full right, power, authority and capacity to enter
into this Purchase Agreement and to consummate the transactions contemplated
hereby and has taken all necessary corporate action to authorize the execution,
delivery and performance of this Purchase Agreement, and this Purchase Agreement
will constitute the valid and binding obligations of Purchaser enforceable
against Purchaser.

         SECTION 4. CLOSING CONDITIONS

         The Purchaser's obligation to purchase the Shares is conditioned on the
following:

         4.1 The representations made by the Company set forth above shall be
true and correct as of the Closing and Purchaser shall have received a
Certificate of the Chief Executive Officer and Corporate Secretary of the
Company to that effect.

         4.2 The Company shall have delivered to the Purchaser a stock
certificate or certificates representing the Shares registered in the name of
the Purchaser or a 100% Affiliate designated by Purchaser.

         4.3 Notwithstanding anything else in this Purchase Agreement, if the
sale and issuance of the Shares is subject to the premerger notification
requirements of the Hart-Scott-Rodino Antitrust Improvements Act of 1976, as
amended (the "HSR Act"), it shall be a condition to the sale of the Shares that
any waiting period under the HSR Act applicable to the purchase of the Shares
shall have expired or been terminated and any approvals required thereunder
shall have been obtained, and the parties shall cooperate in promptly filing
premerger reports and in taking all steps reasonably necessary to obtain early
termination of any applicable HSR Act waiting periods. If any such waiting
period shall not have expired or been subject to early termination on or before
the date ninety (90) days from the date of this Agreement, either party may
terminate this Agreement by giving written notice to the other.



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         4.4 In accordance with and pursuant to the terms of the Alliance
Agreement, the Warrant (as defined therein) shall have been delivered to the
Purchaser.

         4.5 The Company shall have executed a Registration Rights Agreement in
the form attached hereto as Exhibit B and the holders of a majority of the
Registrable Shares (as defined in the Company's Third Amended and Restated
Registration Rights Agreement) shall have consented to the execution thereof by
the Company.

         4.6 In the event of a closing pursuant to Section 1.1 hereof, the
Registration Statement shall have been declared and shall be effective under the
Securities Act of 1933, as amended, by the SEC and no stop order, injunction or
suspension shall have been imposed or threatened with respect to such
Registration Statement.

         4.7 In the event of a closing pursuant to Section 1.2 hereof, from the
date of the execution of this Agreement to the closing, (i) there shall have
been no material adverse change in the business or financial condition of the
Company and the Company shall not have taken any steps to seek protection
pursuant to any bankruptcy law and (ii) no stop order, injunction or suspension
shall have been imposed or threatened with respect to the Registration
Statement.

         SECTION 5. 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,
Purchaser agrees not to sell or otherwise transfer or dispose of any of the
Shares 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.

         SECTION 6. OTHER AGREEMENTS.

         6.1 FURTHER ASSURANCES. The Purchaser and the Company each agrees to
execute such further instruments and to take such further action as may
reasonably be necessary to carry out the intent of this Agreement.

         6.2 CONFIDENTIALITY. The parties hereto acknowledge and agree that they
are bound by the terms of the confidentiality provisions contained in Section 10
of the Alliance Agreement. Notwithstanding the foregoing, Purchaser may disclose
confidential information to any prospective purchaser of the Shares as long as
such prospective purchaser agrees in writing to be bound by the provisions of
such Section 10 of the Alliance Agreement.

         6.3 NOTICES. All notices, requests, consents and other communications
hereunder shall be in writing, shall be addressed to the receiving party's
address set forth above or to such other address as a party may designate by
notice hereunder, and shall be either (i) delivered by hand, (ii) made by
telecopy or facsimile transmission, (iii) sent by overnight


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courier, or (iv) sent by registered mail, return receipt requested, postage
prepaid. All notices, requests, consents and other communications hereunder
shall be deemed to have been given either (i) if by hand, at the time of the
delivery thereof to the receiving party at the address of such party set forth
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 notice is delivered to the courier service, or (iv) if sent by registered
mail, on the 5th business day following the day such mailing is made.

         6.4 ENTIRE AGREEMENT. This Agreement embodies the entire agreement and
understanding between you and the Company with respect to the subject matter
hereof and supersedes all prior oral or written agreements and understandings
relating to the subject matter hereof. No statement, representation, warranty,
covenant or agreement of any kind not expressly set forth in this Agreement
shall affect, or be used to interpret, change or restrict, the express terms and
provisions of this Agreement.

         6.5 MODIFICATIONS AND AMENDMENTS. The terms and provisions of this
Agreement may be modified or amended only by written agreement executed by all
parties hereto.

         6.6 WAIVERS AND CONSENTS. The terms and provisions of this Agreement
may be waived, or consent for the departure therefrom granted, only by written
document executed by the party entitled to the benefits of such terms or
provisions. No such waiver or consent shall be deemed to be or shall constitute
a waiver or consent with respect to any other terms or provisions of this
Agreement, whether or not similar. Each such waiver or consent shall be
effective only in the specific instance and for the purpose for which it was
given, and shall not constitute a continuing waiver or consent.

         6.7 ASSIGNMENT. The rights an obligations under this Agreement may not
be assigned by either party hereto (whether by operation of law or otherwise)
without the prior written consent of the other party; provided, however, that
after the date of the closing, the Company may assign its rights and obligations
hereunder to any person or entity who succeeds to all or substantially all of
the Company's business; provided, further, that either party hereto may assign
its rights and obligations under this Agreement to any 100% Affiliate. For the
purposes of this Section 6.7, "100% Affiliate" shall mean any company,
corporation, business or entity controlled by, controlling, or under common
control with either party to this Purchase Agreement. For this purpose,
"control" means direct or indirect beneficial ownership of one hundred percent
(100%) interest in the voting stock (or the equivalent) of such corporation or
other business.

         6.8 BENEFIT. All statements, representations, warranties, covenants and
agreements in this Agreement shall be binding on the parties hereto and shall
inure to the benefit of the respective successors and permitted assigns of each
party hereto. Nothing in this Agreement shall be construed to create any rights
or obligations except among the parties hereto, and no person or entity shall be
regarded as a third-party beneficiary of this Agreement.


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         6.9 GOVERNING LAW. This Agreement and the rights and obligations of the
parties hereunder shall be construed in accordance with and governed by the law
of the Commonwealth of Massachusetts, without giving effect to the conflict of
law principles thereof.

         6.10 SEVERABILITY. In the event that any court of competent
jurisdiction shall determine that any provision, or any portion thereof,
contained in this Agreement shall be unreasonable or unenforceable in any
respect, then such provision shall be deemed limited to the extent that such
court deems it reasonable and enforceable, and as so limited shall remain in
full force and effect. In the event that such court shall deem any such
provision, or portion thereof, wholly unenforceable, the remaining provisions of
this Agreement shall nevertheless remain in full force and effect.

         6.11 HEADINGS AND CAPTIONS. The headings and captions of the various
subdivisions of this Agreement 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 hereof.

         6.12 NO WAIVER OF RIGHTS, POWERS AND REMEDIES. No failure or delay by
a party hereto in exercising any right, power or remedy under this Agreement,
and no course of dealing between the parties hereto, shall operate as a waiver
of any such right, power or remedy of the party. No single or partial exercise
of any right, power or remedy under this Agreement by a party hereto, nor any
abandonment or discontinuance of steps to enforce any such right, power or
remedy, shall preclude such party from any other or further exercise thereof or
the exercise of any other right, power or remedy hereunder. The election of any
remedy by a party hereto shall not constitute a waiver of the right of such
party to pursue other available remedies. No notice to or demand on a party not
expressly required under this Agreement shall entitle the party receiving such
notice or demand to any other or further notice or demand in similar or other
circumstances or constitute a waiver of the rights of the party giving such
notice or demand to any other or further action in any circumstances without
such notice or demand.

         6.13 SURVIVAL OF REPRESENTATIONS AND WARRANTIES. All representations
and warranties made by the parties hereto in this Purchase Agreement or in any
other agreement, certificate or instrument provided for or contemplated hereby,
shall survive the execution and delivery hereof and any investigations made by
or on behalf of the parties.

         6.14 NO BROKER OR FINDER. Each of the parties hereto represents and
warrants to the other that no broker, finder or other financial consultant has
acted on its behalf in connection with this Purchase Agreement or the
transactions contemplated hereby in such a way as to create any liability on the
other. Each of the parties hereto agrees to indemnify and save the other
harmless from any claim or demand for commission or other compensation by any
broker, finder, financial consultant or similar agent claiming to have been
employed by or on behalf of such party and to bear the cost of legal expenses
incurred in defending against any such claim.

         6.15 COUNTERPARTS. This Agreement may be executed in one or more
counterparts, and by different parties hereto on separate counterparts, each of
which shall be deemed an original, but all of which together shall constitute
one and the same instrument.


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         If the foregoing accurately sets forth your understanding and
agreement, please sign the enclosed copy of this agreement and return it to us.

                                       Very truly yours,

                                       VARIAGENICS, INC.

                                       By:  /s/ Taylor J. Crouch
                                           -----------------------------------
                                       Name:  Taylor J. Crouch
                                       Title: President

Accepted and agreed as of this
21st day of June, 2000

WATERS INVESTMENTS LIMITED

By: /s/ Philip S. Taylor
    -------------------------------
Name:  Philip S. Taylor
Title: Chief Financial Officer


Address:

Waters Investments Limited
109 Lukens Drive
New Castle, DE 19720