<PAGE>   1
                                                                   Exhibit 10.28

                            STOCK PURCHASE AGREEMENT

The Medicines Company
One Cambridge Center
Cambridge, Massachusetts  02142


Ladies & Gentlemen:

     The undersigned, _________________________________(the "Investor"), hereby
confirms its agreement with you as follows:

1.   This Stock Purchase Agreement (the "Agreement") is made as of May 11, 2001
between The Medicines Company, a Delaware corporation (the "Company"), and the
Investor.

2.   The Company has authorized the sale and issuance of up to 4,000,000 shares
(the "Shares") of common stock of the Company, $0.001 par value per share (the
"Common Stock"), to certain investors in a private placement (the "Offering").

3.   The Company and the Investor agree that the Investor will purchase from the
Company and the Company will issue and sell to the Investor ___________ Shares,
for a purchase price of $11.00 per share, or an aggregate purchase price of
$_______________, pursuant to the Terms and Conditions for Purchase of Shares
attached hereto as Annex I and incorporated herein by reference as if fully set
forth herein. Unless otherwise requested by the Investor, certificates
representing the Shares purchased by the Investor will be registered in the
Investor's name and address as set forth below.

4.   The Investor represents that, except as set forth below, (a) it has had no
position, office or other material relationship within the past three years with
the Company or persons known to it to be affiliates of the Company, (b) neither
it, nor any group of which it is a member or to which it is related,
beneficially owns (including the right to acquire or vote) any securities of the
Company and (c) it has no direct or indirect affiliation or association with any
NASD member as of the date hereof. Exceptions:

--------------------------------------------------------------------------------
-------------------------------------------------------------------------------.
 (If no exceptions, write "none." If left blank, response will be deemed to be
                                    "none.")

     Please confirm that the foregoing correctly sets forth the agreement
between us by signing in the space provided below for that purpose. By executing
this Agreement, you acknowledge that the Company may use the information in
paragraph 4 above and the name and address information below in preparation of
the Registration Statement (as defined in Annex 1).

                  [Remainder of Page Intentionally Left Blank]
<PAGE>   2
                  [SIGNATURE PAGE TO STOCK PURCHASE AGREEMENT]

AGREED AND ACCEPTED:

THE MEDICINES COMPANY            Investor:
                                           -------------------------------------

                                 By:
                                     -------------------------------------------

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

                                 Title:
                                        ----------------------------------------

                                 Address:
                                          --------------------------------------

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

                                 Tax ID No.:
                                             -----------------------------------

                                 Contact name:
                                               ---------------------------------

                                 Telephone:
                                            ------------------------------------

                                 Name in which shares should be registered
                                 (if different):

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



                                      -2-
<PAGE>   3

                                     ANNEX I

                   TERMS AND CONDITIONS FOR PURCHASE OF SHARES

     1.   AUTHORIZATION AND SALE OF THE SHARES. Subject to these Terms and
Conditions for Purchase of Shares (the "Terms and Conditions"), the Company has
authorized the sale of up to 4,000,000 Shares. The Company reserves the right to
increase or decrease this number.

     2.   AGREEMENT TO SELL AND PURCHASE THE SHARES; SUBSCRIPTION DATE.

          2.1  At the Closing (as defined in Section 3), the Company will sell
to the Investor, and the Investor will purchase from the Company, upon the terms
and conditions hereinafter set forth, the number of Shares set forth in Section
3 of the Stock Purchase Agreement to which these Terms and Conditions are
attached at the purchase price set forth therein.

          2.2  The Company may enter into the same form of Stock Purchase
Agreement, including these Terms and Conditions, with certain other investors
(the "Other Investors") and expects to complete sales of Shares to them. (The
Investor and the Other Investors are hereinafter sometimes collectively referred
to as the "Investors," and the Stock Purchase Agreement to which these Terms and
Conditions are attached and the Stock Purchase Agreements (including attached
Terms and Conditions) executed by the Other Investors are hereinafter sometimes
collectively referred to as the "Agreements.") The Company may accept executed
Agreements from Investors for the purchase of Shares commencing upon the date on
which the Company provides the Investors with the proposed purchase price per
Share and concluding upon the date (the "Subscription Date") on which the
Company has (i) executed Agreements with Investors for the purchase of at least
4,000,000 Shares, and (ii) notified the Investors in writing that it is no
longer accepting additional Agreements from Investors for the purchase of
Shares. The Company may not enter into any Agreements after the Subscription
Date.

     3.   DELIVERY OF THE SHARES AT CLOSING. The completion of the purchase and
sale of the Shares (the "Closing") shall occur (the "Closing Date") on May 16,
2001, at the offices of the Company's counsel. At the Closing, the Company shall
deliver to the Investor one or more stock certificates representing the number
of Shares set forth in Section 3 of the Stock Purchase Agreement, each such
certificate to be registered in the name of the Investor or, if so indicated on
the signature page hereto, in the name of a nominee designated by the Investor.

     The Company's obligation to issue the Shares to the Investor shall be
subject to the following conditions, any one or more of which may be waived by
the Company: (a) receipt by the Company of a certified or official bank check or
wire transfer of funds in the full amount of the purchase price for the Shares
being purchased hereunder as set forth in Section 3 of the Stock Purchase
Agreement; (b) completion of the purchases and sales under the Agreements with
the Other Investors; and (c) the accuracy of the representations and warranties
made by the Investors and the fulfillment of those undertakings of the Investors
to be fulfilled prior to the Closing.

     The Investor's obligation to purchase the Shares shall be subject to the
following conditions, any one or more of which may be waived by the Investor:
(a) Investors shall have executed Agreements for the purchase of at least
4,000,000 Shares, (b) the representations and warranties of the Company set
forth herein shall be true and correct as of the Closing Date in all material
respects and (c) the Investor shall have received such documents as such
Investor shall reasonably have requested, including, a standard opinion of
Company Counsel as to the matters set forth in Section 4.2 and as to exemption
from the registration requirements of the Securities Act of 1933, as amended
(the "Securities Act"), of the sale of the Shares.

     4.   REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE COMPANY. The Company
hereby represents and warrants to, and covenants with, the Investor, as follows:

          4.1  ORGANIZATION. The Company is duly organized and validly existing
in good standing under the laws of the jurisdiction of its organization. Each of
the Company and its Subsidiaries (as defined in Rule 405 under the Securities
Act) has full power and authority to own, operate and occupy its properties and
to conduct its business as presently conducted and as described in the documents
filed by the Company under the Securities Exchange Act of 1934, as amended (the
"Exchange Act"), since the end of its most recently completed fiscal year
through the date hereof, including, without limitation, its report on Form



                                      -3-
<PAGE>   4

10-K for the year ended December 31, 2000 and its current report on Form 10-Q
for the quarter ended March 31, 2001 (the "Exchange Act Documents"), and is
registered or qualified to do business and in good standing in each jurisdiction
in which the nature of the business conducted by it or the location of its
properties owned or leased by it requires such qualification and where the
failure to be so qualified would have a material adverse effect upon the
condition (financial or otherwise), earnings, business or business prospects,
properties or operations of the Company and its Subsidiaries, considered as one
enterprise (a "Material Adverse Effect"), and no proceeding has been instituted
in any such jurisdiction, revoking, limiting or curtailing, or seeking to
revoke, limit or curtail, such power and authority or qualification.

          4.2  DUE AUTHORIZATION AND VALID ISSUANCE. The Company has all
requisite power and authority to execute, deliver and perform its obligations
under the Agreements, and the Agreements have been duly authorized and validly
executed and delivered by the Company and constitute legal, valid and binding
agreements of the Company enforceable against the Company in accordance with
their terms, except as rights to indemnity and contribution may be limited by
state or federal securities laws or the public policy underlying such laws,
except as enforceability may be limited by applicable bankruptcy, insolvency,
reorganization, moratorium or similar laws affecting creditors' and contracting
parties' rights generally and except as enforceability may be subject to general
principles of equity (regardless of whether such enforceability is considered in
a proceeding in equity or at law). The Shares being purchased by the Investor
hereunder will, upon issuance and payment therefor pursuant to the terms hereof,
be duly authorized, validly issued, fully-paid and nonassessable.

          4.3  NON-CONTRAVENTION. The execution and delivery of the Agreements,
the issuance and sale of the Shares under the Agreements, the fulfillment of the
terms of the Agreements and the consummation of the transactions contemplated
thereby will not (A) conflict with or constitute a violation of, or default
(with the passage of time or otherwise) under, (i) any material bond, debenture,
note or other evidence of indebtedness, lease, contract, indenture, mortgage,
deed of trust, loan agreement, joint venture or other agreement or instrument to
which the Company or any Subsidiary is a party or by which it or any of its
Subsidiaries or their respective properties are bound, (ii) the charter, by-laws
or other organizational documents of the Company or any Subsidiary, or (iii) any
law, administrative regulation, ordinance or order of any court or governmental
agency, arbitration panel or authority applicable to the Company or any
Subsidiary or their respective properties, except in the case of clauses (i) and
(iii) for any such conflicts, violations or defaults which are not reasonably
likely to have a Material Adverse Effect or (B) result in the creation or
imposition of any lien, encumbrance, claim, security interest or restriction
whatsoever upon any of the material properties or assets of the Company or any
Subsidiary or an acceleration of indebtedness pursuant to any obligation,
agreement or condition contained in any material bond, debenture, note or any
other evidence of indebtedness or any material indenture, mortgage, deed of
trust or any other agreement or instrument to which the Company or any
Subsidiary is a party or by which any of them is bound or to which any of the
material property or assets of the Company or any Subsidiary is subject. No
consent, approval, authorization or other order of, or registration,
qualification or filing with, any regulatory body, administrative agency, or
other governmental body in the United States or any other person is required for
the execution and delivery of the Agreements and the valid issuance and sale of
the Shares to be sold pursuant to the Agreements, other than such as have been
made or obtained, and except for any post-closing securities filings or
notifications required to be made under federal or state securities laws.

          4.4  CAPITALIZATION. The capitalization of the Company as of March 31,
2001 is as set forth in the most recent applicable Exchange Act Documents,
increased as set forth in the next sentence. The Company has not issued any
capital stock since that date other than pursuant to (i) employee benefit plans
disclosed in the Exchange Act Documents, or (ii) outstanding warrants, options
or other securities disclosed in the Exchange Act Documents. The Shares to be
sold pursuant to the Agreements have been duly authorized, and when issued and
paid for in accordance with the terms of the Agreements will be duly and validly
issued, fully paid and nonassessable. The outstanding shares of capital stock of
the Company have been duly and validly issued and are fully paid and
nonassessable, have been issued in compliance with all federal and state
securities laws, and were not issued in violation of any preemptive rights or
similar rights to subscribe for or purchase securities. Except as set forth in
or contemplated by the Exchange Act Documents or options granted after March 31,
2001, there are no outstanding rights (including, without limitation, preemptive
rights), warrants or options to acquire, or instruments convertible into or
exchangeable for, any unissued shares of capital stock or other equity interest
in the Company or any Subsidiary, or any contract, commitment, agreement,
understanding or arrangement of any kind to which the Company is a party or of
which the Company has knowledge and relating to the issuance or sale of any
capital stock of the Company or any Subsidiary, any such convertible or
exchangeable securities or any such rights, warrants or options. Without
limiting the foregoing, except as set forth in the Exchange Act Documents, no
preemptive right, co-sale right, right of first refusal, registration right, or
other similar right exists with respect to the Shares or the issuance and sale
thereof. No further approval or authorization of any stockholder, the Board of
Directors of the



                                      -4-
<PAGE>   5

Company or others is required for the issuance and sale of the Shares. The
Company owns the entire equity interest in each of its Subsidiaries, free and
clear of any pledge, lien, security interest, encumbrance, claim or equitable
interest, other than as described in the Exchange Act Documents. Except as
disclosed in the Exchange Act Documents, there are no stockholders agreements,
voting agreements or other similar agreements with respect to the Common Stock
to which the Company is a party or, to the knowledge of the Company, between or
among any of the Company's stockholders.

          4.5  LEGAL PROCEEDINGS. There is no material legal or governmental
proceeding pending or, to the knowledge of the Company, threatened to which the
Company or any Subsidiary is or may be a party or of which the business or
property of the Company or any Subsidiary is subject that is not disclosed in
the Exchange Act Documents.

          4.6  NO VIOLATIONS. Neither the Company nor any Subsidiary is in
violation of its charter, bylaws, or other organizational document, or in
violation of any law, administrative regulation, ordinance or order of any court
or governmental agency, arbitration panel or authority applicable to the Company
or any Subsidiary, which violation, individually or in the aggregate, would be
reasonably likely to have a Material Adverse Effect, or is in default (and there
exists no condition which, with the passage of time or otherwise, would
constitute a default) in any material respect in the performance of any bond,
debenture, note or any other evidence of indebtedness in any indenture,
mortgage, deed of trust or any other material agreement or instrument to which
the Company or any Subsidiary is a party or by which the Company or any
Subsidiary is bound or by which the properties of the Company or any Subsidiary
are bound, which would be reasonably likely to have a Material Adverse Effect
upon the business or financial condition of the Company and its Subsidiaries,
considered as one enterprise.

          4.7  GOVERNMENTAL PERMITS, ETC. Each of the Company and its
Subsidiaries has all necessary franchises, licenses, certificates, permits and
other authorizations from any foreign, federal, state or local government or
governmental agency, department, or body that are currently necessary for the
operation of the business of the Company and its Subsidiaries as currently
conducted and as described in the Exchange Act Documents except where the
failure to currently possess could not reasonably be expected to have a Material
Adverse Effect.

          4.8  INTELLECTUAL PROPERTY. Except as specifically disclosed in the
Exchange Act Documents (i) each of the Company and its Subsidiaries owns or
possesses sufficient rights to use all material patents, patent rights,
trademarks, copyrights, licenses, inventions, trade secrets, trade names and
know-how (collectively, "Intellectual Property") described or referred to in the
Exchange Act Documents as owned or possessed by it or that are necessary for the
conduct of its business as now conducted or as proposed to be conducted as
described in the Exchange Act Documents except where the failure to currently
own or possess would not have a Material Adverse Effect, (ii) neither the
Company nor any of its Subsidiaries has received any notice of infringement, or
to the best knowledge of the Company after due inquiry neither the Company nor
any of its Subsidiaries is infringing, or has any knowledge of, any asserted
infringement by the Company or any of its Subsidiaries of, any rights of a third
party with respect to any Intellectual Property that, individually or in the
aggregate, would have a Material Adverse Effect and (iii) neither the Company
nor any of its Subsidiaries has received any notice of, or has any knowledge of,
infringement by a third party with respect to any Intellectual Property rights
of the Company or of any Subsidiary that, individually or in the aggregate,
would have a Material Adverse Effect.

          4.9  FINANCIAL STATEMENTS. The financial statements of the Company and
the related notes contained in the Exchange Act Documents present fairly, in
accordance with generally accepted accounting principles, the financial position
of the Company and its Subsidiaries as of the dates indicated, and the results
of its operations and cash flows for the periods therein specified consistent
with the books and records of the Company and its Subsidiaries except that
unaudited interim financial statements were or are subject to normal and
recurring year-end adjustments which are not expected to be material in amount.
Such financial statements (including the related notes) have been prepared in
accordance with generally accepted accounting principles applied on a consistent
basis throughout the periods therein specified, except as may be included in the
notes to such financial statements, or the case of unaudited statements, as may
be permitted by the SEC on Form 10-Q under the Exchange Act and except as
disclosed in the Exchange Act Documents. The other financial information
contained in the Exchange Act Documents has been prepared on a basis consistent
with the financial statements of the Company.

          4.10 NO MATERIAL ADVERSE CHANGE. Except as disclosed in the Exchange
Act Documents, since March 31, 2001, there has not been (i) any material adverse
change in the financial condition or earnings of the Company and its
Subsidiaries considered as one enterprise, (ii) any material adverse event
affecting the Company or its Subsidiaries, (iii) any obligation, direct or
contingent, that is material to the Company and its Subsidiaries considered as
one enterprise, incurred by the Company, except



                                      -5-
<PAGE>   6

obligations incurred in the ordinary course of business, (iv) any dividend or
distribution of any kind declared, paid or made on the capital stock of the
Company or any of its Subsidiaries, or (v) any loss or damage (whether or not
insured) to the physical property of the Company or any of its Subsidiaries
which has been sustained which has a Material Adverse Effect.

          4.11 DISCLOSURE. The representations and warranties of the Company
contained in this Section 4 as of the date hereof and as of the Closing Date,
did not and shall not 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, in light of the circumstances under which they were made,
not misleading. In addition, since January 5, 2001, the date that the Company
filed its registration statement on Form S-1 which was subsequently withdrawn on
March 19, 2001, there have been no changes in the Company's business or
financial condition that are material to the investment decision of the Investor
in the Offering and have not been disclosed in the Exchange Act Documents.

          4.12 NASDAQ COMPLIANCE. The Company's Common Stock is registered
pursuant to Section 12(g) of the Exchange Act and is listed on The Nasdaq Stock
Market, Inc. National Market (the "Nasdaq National Market"), and the Company has
taken no action designed to, or likely to have the effect of, terminating the
registration of the Common Stock under the Exchange Act or de-listing the Common
Stock from the Nasdaq National Market, nor has the Company received any
notification that the Securities and Exchange Commission (the "SEC") or the
National Association of Securities Dealers, Inc. ("NASD") is contemplating
terminating such registration or listing.

          4.13 REPORTING STATUS. The Company has filed in a timely manner all
documents that the Company was required to file under the Exchange Act during
the period from August 8, 2000, the closing date of the Company's initial public
offering, to the date of this Agreement. The following documents complied in all
material respects with the SEC's requirements as of their respective filing
dates, and the information contained therein as of the date thereof did not
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 in
light of the circumstances under which they were made not misleading:

               (a)  amendment no. 1 to the proxy statement pursuant to Section
                    14(a) of the Exchange Act, filed on May 3, 2001;

               (b)  the proxy statement pursuant to Section 14(a) of the
                    Exchange Act, filed on April 30, 2001;

               (c)  the annual report on Form 10-K for the year ended December
                    31, 2000, filed on April 2, 2001;

               (d)  the quarterly report on Form 10-Q for the quarter ended
                    March 31, 2001 filed on May 10, 2001;

               (e)  the quarterly report on Form 10-Q for the quarter ended
                    September 30, 2001, filed on November 8, 2001;

               (f)  the quarterly report on Form 10-Q for the quarter ended June
                    30, 2000, filed on September 19, 2000;

               (g)  the registration on Form 8-A, under the Exchange Act, filed
                    July 28, 2000; and

               (h)  All other documents, if any, filed by the Company with the
                    SEC since August 8, 2000 pursuant to the reporting
                    requirements of the Exchange Act.

          4.14 LISTING. The Company shall comply with all requirements of the
National Association of Securities Dealers, Inc. with respect to the issuance of
the Shares and the listing thereof on the Nasdaq National Market.

          4.15 NO MANIPULATION OF STOCK. The Company has not taken and will not,
in violation of applicable law, take, any action designed to or that might
reasonably be expected to cause or result in stabilization or manipulation of
the price of the Common Stock to facilitate the sale or resale of the Shares.



                                      -6-
<PAGE>   7

          4.16 COMPANY NOT AN "INVESTMENT COMPANY". The Company has been advised
of the rules and requirements under the Investment Company Act of 1940, as
amended (the "Investment Company Act"). The Company is not, and immediately
after receipt of payment for the Shares will not be, an "investment company" or
an entity "controlled" by an "investment company" within the meaning of the
Investment Company Act and shall conduct its business in a manner so that it
will not become subject to the Investment Company Act.

     5.   REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE INVESTOR.

          5.1  The Investor represents and warrants to, and covenants with, the
Company that: (i) the Investor is an "accredited investor" as defined in
Regulation D under the Securities Act and the Investor is also knowledgeable,
sophisticated and experienced in making, and is qualified to make decisions with
respect to investments in shares presenting an investment decision like that
involved in the purchase of the Shares, including investments in securities
issued by the Company and investments in comparable companies, and has
requested, received, reviewed and considered all information it deemed relevant
in making an informed decision to purchase the Shares; (ii) the Investor is
acquiring the number of Shares set forth in Section 3 of the Stock Purchase
Agreement in the ordinary course of its business and for its own account for
investment only and with no present intention of distributing any of such Shares
or any arrangement or understanding with any other persons regarding the
distribution of such Shares; (iii) the Investor will not, directly or
indirectly, offer, sell, pledge, transfer or otherwise dispose of (or solicit
any offers to buy, purchase or otherwise acquire or take a pledge of) any of the
Shares except in compliance with the Securities Act, applicable state securities
laws and the respective rules and regulations promulgated thereunder; (iv) the
Investor has answered all questions on the Investor Questionnaire for use in
preparation of the Registration Statement and the answers thereto are true,
correct and complete as of the date hereof and will be true, correct and
complete as of the Closing Date; (v) the Investor will notify the Company
immediately of any change in any of such information until such time as the
Investor has sold all of its Shares or until the Company is no longer required
to keep the Registration Statement effective; and (vi) the Investor has, in
connection with its decision to purchase the number of Shares set forth in
Section 3 of the Stock Purchase Agreement, relied only upon the Exchange Act
Documents and the representations and warranties of the Company contained
herein. The Investor understands that its acquisition of the Shares has not been
registered under the Securities Act or registered or qualified under any state
securities law in reliance on specific exemptions therefrom, which exemptions
may depend upon, among other things, the bona fide nature of the Investor's
investment intent as expressed herein. Investor has completed or caused to be
completed and delivered to the Company the Investor Questionnaire, which
questionnaire is true, correct and complete in all material respects.

          5.2  The Investor acknowledges, represents and agrees that no action
has been or will be taken in any jurisdiction outside the United States by the
Company that would permit an offering of the Shares, or possession or
distribution of offering materials in connection with the issue of the Shares,
in any jurisdiction outside the United States where legal action by the Company
for that purpose is required. Each Investor outside the United States will
comply with all applicable laws and regulations in each foreign jurisdiction in
which it purchases, offers, sells or delivers Shares or has in its possession or
distributes any offering material, in all cases at its own expense.

          5.3  The Investor hereby covenants with the Company not to make any
sale of the Shares without complying with the provisions of this Agreement and
without causing the prospectus delivery requirement under the Securities Act to
be satisfied, and the Investor acknowledges that the certificates evidencing the
Shares will be imprinted with a legend that prohibits their transfer except in
accordance therewith. The Investor acknowledges that there may occasionally be
times when the Company determines that it must suspend the use of the Prospectus
forming a part of the Registration Statement, as set forth in Section 7.2(c).

          5.4  The Investor further represents and warrants to, and covenants
with, the Company that (i) the Investor has full right, power, authority and
capacity to enter into this Agreement and to consummate the transactions
contemplated hereby and has taken all necessary action to authorize the
execution, delivery and performance of this Agreement, and (ii) this Agreement
constitutes a valid and binding obligation of the Investor enforceable against
the Investor in accordance with its terms, except as enforceability may be
limited by applicable bankruptcy, insolvency, reorganization, moratorium or
similar laws affecting creditors' and contracting parties' rights generally and
except as enforceability may be subject to general principles of equity
(regardless of whether such enforceability is considered in a proceeding in
equity or at law) and except as the indemnification agreements of the Investors
herein may be legally unenforceable.


                                      -7-
<PAGE>   8

          5.5  Investor will not use any of the restricted Shares acquired
pursuant to this Agreement to cover any short position in the Common Stock of
the Company if doing so would be in violation of applicable securities laws.

          5.6  The Investor understands that nothing in the Exchange Act
Documents, this Agreement or any other materials presented to the Investor in
connection with the purchase and sale of the Shares constitutes legal, tax or
investment advice. The Investor has consulted such legal, tax and investment
advisors as it, in its sole discretion, has deemed necessary or appropriate in
connection with its purchase of Shares.

          5.7  The Investor understands that the Company filed a registration
statement on Form S-1 under the Securities Act on January 5, 2001, as amended on
January 26, 2001 and February 23, 2001, for a public offering of shares of the
Company's Common Stock, that such public offering was never completed and has
been abandoned and that such registration statement was withdrawn on March 19,
2001. The Investor understands that the Shares have not been registered under
the Securities Act by reason of their issuance in a transaction exempt from the
registration requirements of the Securities Act pursuant to Section 4(2) or
Regulation D promulgated thereunder and, as a result, the Investor will not have
the protection of Section 11 of the Securities Act (15 U.S.C. 77k) with respect
to the purchase of the Shares.

     6.   SURVIVAL OF REPRESENTATIONS, WARRANTIES AND AGREEMENTS.
Notwithstanding any investigation made by any party to this Agreement, all
covenants, agreements, representations and warranties made by the Company and
the Investor herein shall survive the execution of this Agreement, the delivery
to the Investor of the Shares being purchased and the payment therefor.

     7.   REGISTRATION OF THE SHARES; COMPLIANCE WITH THE SECURITIES ACT.

          7.1  REGISTRATION PROCEDURES AND OTHER MATTERS. The Company shall:

               (a)  subject to receipt of necessary information from the
Investors after prompt request from the Company to the Investors to provide such
information, prepare and file with the SEC, within 10 days after the Closing
Date, a registration statement on Form S-1 (the "S-1 Registration Statement") to
enable the resale of the Shares by the Investors from time to time through the
automated quotation system of the Nasdaq National Market or in
privately-negotiated transactions;

               (b)  use its reasonable best efforts, subject to receipt of
necessary information from the Investors after prompt request from the Company
to the Investors to provide such information, to cause the S-1 Registration
Statement to become effective within 30 days after the S-1 Registration
Statement is filed by the Company such efforts to include, without limiting the
generality of the foregoing, preparing and filing with the SEC in such 30-day
period any financial statements that are required to be filed prior to the
effectiveness of such S-1 Registration Statement;

               (c)  use its reasonable best efforts, subject to receipt of
necessary information from the Investors after prompt request from the Company
to the Investors to provide such information, to prepare and file with the SEC,
within 10 days after the Company first becomes eligible to file a registration
statement on Form S-3, a registration statement on Form S-3 (the "S-3
Registration Statement") to enable the resale of the Shares by the Investors
from time to time through the automated quotation system of the Nasdaq National
Market or in privately-negotiated transactions; and to use its reasonable best
efforts to cause the S-3 Registration Statement to become effective as soon as
practicable thereafter, such efforts to include, without limiting the generality
of the foregoing, preparing and filing with the SEC as promptly as practicable
any financial statements that are required to be filed prior to the
effectiveness of such S-3 Registration Statement (the term "Registration
Statement" shall mean the S-1 Registration Statement until the S-3 Registration
Statement is declared effective by the SEC, after which time it shall mean the
S-3 Registration Statement).

               (d)  use its reasonable best efforts to prepare and file with the
SEC such amendments and supplements to the Registration Statement and the
Prospectus used in connection therewith as may be necessary to keep the
Registration Statement current, effective and free from any material
misstatement or omission to state a material fact for a period not exceeding,
with respect to each Investor's Shares purchased hereunder, the earlier of (i)
the second anniversary of the Closing Date, (ii) the date on which the Investor
may sell all Shares then held by the Investor without restriction by the volume
limitations of Rule 144(e) of the Securities Act, or (iii) such time as all
Shares purchased by such Investor in this Offering have been sold pursuant to a
registration statement;



                                      -8-
<PAGE>   9

               (e)  furnish to the Investor with respect to the Shares
registered under the Registration Statement such number of copies of the
Registration Statement, Prospectuses and Preliminary Prospectuses in conformity
with the requirements of the Securities Act and such other documents as the
Investor may reasonably request, in order to facilitate the public sale or other
disposition of all or any of the Shares by the Investor; provided, however, that
the obligation of the Company to deliver copies of Prospectuses or Preliminary
Prospectuses to the Investor shall be subject to the receipt by the Company of
reasonable assurances from the Investor that the Investor will comply with the
applicable provisions of the Securities Act and of such other securities or blue
sky laws as may be applicable in connection with any use of such Prospectuses or
Preliminary Prospectuses;

               (f)  file documents required of the Company for normal blue sky
clearance in states specified in writing by the Investor and use its reasonable
best efforts to maintain such blue sky qualifications during the period the
Company is required to maintain the effectiveness of the Registration Statement
pursuant to Section 7.1(d); provided, however, that the Company shall not be
required to qualify to do business or consent to service of process in any
jurisdiction in which it is not now so qualified or has not so consented;

               (g)  bear all expenses in connection with the procedures in
paragraph (a) through (f) of this Section 7.1 and the registration of the Shares
pursuant to the Registration Statement; and

               (h)  advise the Investor, promptly after it shall receive notice
or obtain knowledge of the issuance of any stop order by the SEC delaying or
suspending the effectiveness of the Registration Statement or of the initiation
or threat of any proceeding for that purpose; and it will promptly use its
reasonable best efforts to prevent the issuance of any stop order or to obtain
its withdrawal at the earliest possible moment if such stop order should be
issued.

     Notwithstanding anything to the contrary herein, the Registration Statement
shall cover only the Shares. In no event at any time before the Registration
Statement becomes effective with respect to the Shares shall the Company
publicly announce or file any other registration statement, other than
registration statements on Form S-8, without the prior written consent of a
majority in interest of the Investors.

     The Company understands that the Investor disclaims being an underwriter,
but the Investor being deemed an underwriter by the SEC shall not relieve the
Company of any obligations it has hereunder; PROVIDED, HOWEVER that if the
Company receives notification from the SEC that the Investor is deemed an
underwriter, then the period by which the Company is obligated to submit an
acceleration request to the SEC shall be extended to the earlier of (i) the 90th
day after such SEC notification, or (ii) 120 days after the initial filing of
the Registration Statement with the SEC.

          7.2  TRANSFER OF SHARES AFTER REGISTRATION; SUSPENSION.

               (a)  The Investor agrees that it will not effect any disposition
of the Shares or its right to purchase the Shares that would constitute a sale
within the meaning of the Securities Act except as contemplated in the
Registration Statement referred to in Section 7.1 and as described below or as
otherwise permitted by law, and that it will promptly notify the Company of any
changes in the information set forth in the Registration Statement regarding the
Investor or its plan of distribution.

               (b)  Except in the event that paragraph (c) below applies, the
Company shall (i) if deemed necessary by the Company, prepare and file from time
to time with the SEC a post-effective amendment to the Registration Statement or
a supplement to the related Prospectus or a supplement or amendment to any
document incorporated therein by reference or file any other required document
so that such Registration Statement will not 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 so that, as
thereafter delivered to purchasers of the Shares being sold thereunder, such
Prospectus will not 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, in light of the circumstances under which they were made,
not misleading; (ii) provide the Investor copies of any documents filed pursuant
to Section 7.2(b)(i); and (iii) inform each Investor that the Company has
complied with its obligations in Section 7.2(b)(i) (or that, if the Company has
filed a post-effective amendment to the Registration Statement which has not yet
been declared effective, the Company will notify the Investor to that effect,
will use its reasonable best efforts to secure the effectiveness of such


                                      -9-
<PAGE>   10

post-effective amendment as promptly as possible and will promptly notify the
Investor pursuant to Section 7.2(b)(i) hereof when the amendment has become
effective).

               (c)  Subject to paragraph (d) below, in the event (i) of any
request by the SEC or any other federal or state governmental authority during
the period of effectiveness of the Registration Statement for amendments or
supplements to a Registration Statement or related Prospectus or for additional
information; (ii) of the issuance by the SEC or any other federal or state
governmental authority of any stop order suspending the effectiveness of a
Registration Statement or the initiation of any proceedings for that purpose;
(iii) of the receipt by the Company of any notification with respect to the
suspension of the qualification or exemption from qualification of any of the
Shares for sale in any jurisdiction or the initiation or threatening of any
proceeding for such purpose; or (iv) of any event or circumstance which, upon
the advice of its counsel, necessitates the making of any changes in the
Registration Statement or Prospectus, or any document incorporated or deemed to
be incorporated therein by reference, so that, in the case of the Registration
Statement, it will not contain any untrue statement of a material fact or any
omission to state a material fact required to be stated therein or necessary to
make the statements therein not misleading, and that in the case of the
Prospectus, it will not contain any untrue statement of a material fact or any
omission to state a material fact required to be stated therein or necessary to
make the statements therein, in the light of the circumstances under which they
were made, not misleading; then the Company shall deliver a certificate in
writing to the Investor (the "Suspension Notice") to the effect of the foregoing
and, upon receipt of such Suspension Notice, the Investor will refrain from
selling any Shares pursuant to the Registration Statement (a "Suspension") until
the Investor's receipt of copies of a supplemented or amended Prospectus
prepared and filed by the Company, or until it is advised in writing by the
Company that the current Prospectus may be used, and has received copies of any
additional or supplemental filings that are incorporated or deemed incorporated
by reference in any such Prospectus. In the event of any Suspension, the Company
will use its reasonable best efforts to cause the use of the Prospectus so
suspended to be resumed as soon as reasonably practicable within 20 business
days after the delivery of a Suspension Notice to the Investor. In addition to
and without limiting any other remedies (including, without limitation, at law
or at equity) available to the Investor, the Investor shall be entitled to
specific performance in the event that the Company fails to comply with the
provisions of this Section 7.2(c).

               (d)  Notwithstanding the foregoing paragraphs of this Section
7.2, the Investor shall not be prohibited from selling Shares under the
Registration Statement as a result of Suspensions on more than two occasions of
not more than 30 days each in any twelve month period, unless, in the good faith
judgment of the Company's Board of Directors, upon the written opinion of
counsel of counsel, the sale of Shares under the Registration Statement in
reliance on this paragraph 7.2(d) would be reasonably likely to cause a
violation of the Securities Act or the Exchange Act and result in liability to
the Company.

               (e)  Provided that a Suspension is not then in effect, the
Investor may sell Shares under the Registration Statement, provided that it
arranges for delivery of a current Prospectus to the transferee of such Shares.
Upon receipt of a request therefor, the Company has agreed to provide an
adequate number of current Prospectuses to the Investor and to supply copies to
any other parties requiring such Prospectuses.

               (f)  In the event of a sale of Shares by the Investor pursuant to
the Registration Statement, the Investor must also deliver to the Company's
transfer agent, with a copy to the Company, a Certificate of Subsequent Sale
substantially in the form attached hereto as EXHIBIT A, so that the Shares may
be properly transferred.

          7.3  INDEMNIFICATION. For the purpose of this Section 7.3:

          (i)  the term "Selling Stockholder" shall include the Investor and any
affiliate of such Investor;

          (ii) the term "Registration Statement" shall include the Prospectus in
the form first filed with the SEC pursuant to Rule 424(b) of the Securities Act
or filed as part of the Registration Statement at the time of effectiveness if
no Rule 424(b) filing is required, exhibit, supplement or amendment included in
or relating to the Registration Statement referred to in Section 7.1; and

          (iii) the term "untrue statement" shall include any untrue statement
or alleged untrue statement, or any omission or alleged omission to state in the
Registration Statement a material fact required to be stated therein or
necessary to make the statements therein, in the light of the circumstances
under which they were made, not misleading.



                                      -10-
<PAGE>   11

               (a)  The Company agrees to indemnify and hold harmless each
Selling Stockholder from and against any losses, claims, damages or liabilities
to which such Selling Stockholder may become subject (under the Securities Act
or otherwise) insofar as such losses, claims, damages or liabilities (or actions
or proceedings in respect thereof) arise out of, or are based upon (i) any
breach of the representations or warranties of the Company contained herein or
failure to comply with the covenants and agreements of the Company contained
herein, (ii) any untrue statement of a material fact contained in the
Registration Statement as amended at the time of effectiveness or any omission
of a material fact required to be stated therein or necessary to make the
statements therein not misleading, or (iii) any failure by the Company to
fulfill any undertaking included in the Registration Statement as amended at the
time of effectiveness, and the Company will reimburse such Selling Stockholder
for any reasonable legal or other expenses reasonably incurred in investigating,
defending or preparing to defend any such action, proceeding or claim, or
preparing to defend any such action, proceeding or claim, PROVIDED, HOWEVER,
that the Company shall not be liable in any such case to the extent that such
loss, claim, damage or liability arises out of, or is based upon, an untrue
statement made in such Registration Statement or any omission of a material fact
required to be stated therein or necessary to make the statements therein not
misleading in reliance upon and in conformity with written information furnished
to the Company by or on behalf of such Selling Stockholder specifically for use
in preparation of the Registration Statement or the failure of such Selling
Stockholder to comply with its covenants and agreements contained in Section 7.2
hereof respecting sale of the Shares or any statement or omission in any
Prospectus that is corrected in any subsequent Prospectus that was delivered to
the Selling Stockholder prior to the pertinent sale or sales by the Selling
Stockholder. The Company shall reimburse each Selling Stockholder for the
amounts provided for herein on demand as such expenses are incurred.

               (b)  The Investor agrees to indemnify and hold harmless the
Company (and each person, if any, who controls the Company within the meaning of
Section 15 of the Securities Act, each officer of the Company who signs the
Registration Statement and each director of the Company) from and against any
losses, claims, damages or liabilities to which the Company (or any such
officer, director or controlling person) may become subject (under the
Securities Act or otherwise), insofar as such losses, claims, damages or
liabilities (or actions or proceedings in respect thereof) arise out of, or are
based upon, (i) any failure to comply with the covenants and agreements
contained in Section 7.2 hereof respecting sale of the Shares, or (ii) any
untrue statement of a material fact contained in the Registration Statement or
any omission of a material fact required to be stated therein or necessary to
make the statements therein not misleading if such untrue statement or omission
was made in reliance upon and in conformity with written information furnished
by or on behalf of the Investor specifically for use in preparation of the
Registration Statement, and the Investor will reimburse the Company (or such
officer, director or controlling person), as the case may be, for any legal or
other expenses reasonably incurred in investigating, defending or preparing to
defend any such action, proceeding or claim; provided that the Investor's
obligation to indemnify the Company shall be limited to the net amount received
by the Investor from the sale of the Shares.

               (c)  Promptly after receipt by any indemnified person of a notice
of a claim or the beginning of any action in respect of which indemnity is to be
sought against an indemnifying person pursuant to this Section 7.3, such
indemnified person shall notify the indemnifying person in writing of such claim
or of the commencement of such action, but the omission to so notify the
indemnifying person will not relieve it from any liability which it may have to
any indemnified person under this Section 7.3 (except to the extent that such
omission materially and adversely affects the indemnifying person's ability to
defend such action) or from any liability otherwise than under this Section 7.3.
Subject to the provisions hereinafter stated, in case any such action shall be
brought against an indemnified person, the indemnifying person shall be entitled
to participate therein, and, to the extent that it shall elect by written notice
delivered to the indemnified person promptly after receiving the aforesaid
notice from such indemnified person, shall be entitled to assume the defense
thereof, with counsel reasonably satisfactory to such indemnified person. After
notice from the indemnifying person to such indemnified person of its election
to assume the defense thereof, such indemnifying person shall not be liable to
such indemnified person for any legal expenses subsequently incurred by such
indemnified person in connection with the defense thereof, PROVIDED, HOWEVER,
that if there exists or shall exist a conflict of interest that would make it
inappropriate, in the opinion of counsel to the indemnified person, for the same
counsel to represent both the indemnified person and such indemnifying person or
any affiliate or associate thereof, the indemnified person shall be entitled to
retain its own counsel at the expense of such indemnifying person; provided,
however, that no indemnifying person shall be responsible for the fees and
expenses of more than one separate counsel (together with appropriate local
counsel) for all indemnified parties. In no event shall any indemnifying person
be liable in respect of any amounts paid in settlement of any action unless the
indemnifying person shall have approved the terms of such settlement; PROVIDED
that such consent shall not be unreasonably withheld. No indemnifying person
shall, without the prior written consent of the indemnified person, effect any
settlement of any pending or threatened proceeding in respect of which any
indemnified person is or could have been a party and



                                      -11-
<PAGE>   12

indemnification could have been sought hereunder by such indemnified person,
unless such settlement includes an unconditional release of such indemnified
person from all liability on claims that are the subject matter of such
proceeding.

               (d)  If the indemnification provided for in this Section 7.3 is
unavailable to or insufficient to hold harmless an indemnified person under
subsection (a) or (b) above in respect of any losses, claims, damages or
liabilities (or actions or proceedings in respect thereof) referred to therein,
then each indemnifying person shall contribute to the amount paid or payable by
such indemnified person as a result of such losses, claims, damages or
liabilities (or actions in respect thereof) in such proportion as is appropriate
to reflect the relative fault of the Company on the one hand and the Investor,
as well as any other Selling Shareholders under such registration statement on
the other in connection with the statements or omissions or other matters which
resulted in such losses, claims, damages or liabilities (or actions in respect
thereof), as well as any other relevant equitable considerations. The relative
fault shall be determined by reference to, among other things, in the case of an
untrue statement, whether the untrue statement relates to information supplied
by the Company on the one hand or an Investor or other Selling Shareholder on
the other and the parties' relative intent, knowledge, access to information and
opportunity to correct or prevent such untrue statement. The Company and the
Investor agree that it would not be just and equitable if contribution pursuant
to this subsection (d) were determined by pro rata allocation (even if the
Investor and other Selling Shareholders were treated as one entity for such
purpose) or by any other method of allocation which does not take into account
the equitable considerations referred to above in this subsection (d). The
amount paid or payable by an indemnified person as a result of the losses,
claims, damages or liabilities (or actions in respect thereof) referred to above
in this subsection (d) shall be deemed to include any legal or other expenses
reasonably incurred by such indemnified person in connection with investigating
or defending any such action or claim. Notwithstanding the provisions of this
subsection (d), the Investor shall not be required to contribute any amount in
excess of the amount by which the net amount received by the Investor from the
sale of the Shares to which such loss relates exceeds the amount of any damages
which such Investor has otherwise been required to pay by reason of such untrue
statement. 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. The
Investor's obligations in this subsection to contribute shall be in proportion
to its Investor sale of Shares to which such loss relates and shall not be joint
with any other Selling Shareholders.

               (e)  The parties to this Agreement hereby acknowledge that they
are sophisticated business persons who were represented by counsel during the
negotiations regarding the provisions hereof including, without limitation, the
provisions of this Section 7.3, and are fully informed regarding said
provisions. They further acknowledge that the provisions of this Section 7.3
fairly allocate the risks in light of the ability of the parties to investigate
the Company and its business in order to assure that adequate disclosure is made
in the Registration Statement as required by the Act and the Exchange Act. The
parties are advised that federal or state public policy as interpreted by the
courts in certain jurisdictions may be contrary to certain of the provisions of
this Section 7.3, and the parties hereto hereby expressly waive and relinquish
any right or ability to assert such public policy as a defense to a claim under
this Section 7.3 and further agree not to attempt to assert any such defense.

          7.4  TERMINATION OF CONDITIONS AND OBLIGATIONS. The conditions
precedent imposed by Section 5 or this Section 7 upon the transferability of the
Shares shall cease and terminate as to any particular number of the Shares when
such Shares shall have been effectively registered under the Securities Act and
sold or otherwise disposed of in accordance with the intended method of
disposition set forth in the Registration Statement covering such Shares or at
such time as an opinion of counsel reasonably satisfactory to the Company shall
have been rendered to the effect that such conditions are not necessary in order
to comply with the Securities Act.

          7.5  INFORMATION AVAILABLE. So long as the Registration Statement is
effective covering the resale of Shares owned by the Investor, the Company will
furnish to the Investor:

               (a)  as soon as practicable after it is available, one copy of
(i) its Annual Report to Stockholders (which Annual Report shall contain
financial statements audited in accordance with generally accepted accounting
principles by a national firm of certified public accountants), (ii) its Annual
Report on Form 10-K and (iii) its Quarterly Reports on Form 10-Q (the foregoing,
in each case, excluding exhibits);

               (b)  upon the request of the Investor, all exhibits excluded by
the parenthetical to subparagraph (a) of this Section 7.5 as filed with the SEC
and all other information that is made available to shareholders; and



                                      -12-
<PAGE>   13

               (c)  upon the reasonable request of the Investor, an adequate
number of copies of the Prospectuses to supply to any other party requiring such
Prospectuses; and upon the reasonable request of the Investor, the President or
the Chief Financial Officer of the Company (or an appropriate designee thereof)
will meet with the Investor or a representative thereof at the Company's
headquarters to discuss all information relevant for disclosure in the
Registration Statement covering the Shares and will otherwise cooperate with any
Investor conducting an investigation for the purpose of reducing or eliminating
such Investor's exposure to liability under the Securities Act, including the
reasonable production of information at the Company's headquarters; provided,
that the Company shall not be required to disclose any confidential information
to or meet at its headquarters with any Investor until and unless the Investor
shall have entered into a confidentiality agreement in form and substance
reasonably satisfactory to the Company with the Company with respect thereto.

     8.   NOTICES. All notices, requests, consents and other communications
hereunder shall be in writing, shall be mailed (A) if within the United States
by first-class registered or certified airmail, or nationally recognized
overnight express courier, postage prepaid, or by facsimile, or (B) if delivered
from outside the United States, by International Federal Express or facsimile,
and shall be deemed given (i) if delivered by first-class registered or
certified mail, three business days after so mailed, (ii) if delivered by
nationally recognized overnight carrier, one business day after so mailed, (iii)
if delivered by International Federal Express, two business days after so
mailed, (iv) if delivered by facsimile, upon electronic confirmation of receipt
and shall be delivered as addressed as follows:

          (a)  if to the Company, to:

               The Medicines Company
               One Cambridge Center
               Cambridge, Massachusetts  02142
               Attn:  Clive A. Meanwell

          (b)  with a copy to:

               Hale and Dorr LLP
               60 State Street
               Boston, Massachusetts  02109
               Attn:  Stuart M. Falber, Esq.

          (c)  if to the Investor, at its address on the signature page hereto,
               or at such other address or addresses as may have been furnished
               to the Company in writing.

     9.   CHANGES. This Agreement may not be modified or amended except pursuant
to an instrument in writing signed by the Company and the Investor.

     10.  HEADINGS. The headings of the various sections of this Agreement have
been inserted for convenience of reference only and shall not be deemed to be
part of this Agreement.

     11.  SEVERABILITY. In case any provision contained in this Agreement should
be invalid, illegal or unenforceable in any respect, the validity, legality and
enforceability of the remaining provisions contained herein shall not in any way
be affected or impaired thereby.

     12.  GOVERNING LAW. This Agreement shall be governed by, and construed in
accordance with, the internal laws of the State of Delaware, without giving
effect to the principles of conflicts of law.

     13.  COUNTERPARTS. This Agreement may be executed in two or more
counterparts, each of which shall constitute an original, but all of which, when
taken together, shall constitute but one instrument, and shall become effective
when one or more counterparts have been signed by each party hereto and
delivered to the other parties.



                                      -13-
<PAGE>   14

     14.  RULE 144. The Company covenants that it will timely file the reports
required to be filed by it under the Securities Act and the Exchange Act and the
rules and regulations adopted by the SEC thereunder (or, if the Company is not
required to file such reports, it will, upon the request of any Investor holding
Shares purchased hereunder made after the first anniversary of the Closing Date,
make publicly available such information as necessary to permit sales pursuant
to Rule 144 under the Securities Act), and it will take such further action as
any such Investor may reasonably request, all to the extent required from time
to time to enable such Investor to sell Shares purchased hereunder without
registration under the Securities Act within the limitation of the exemptions
provided by (a) Rule 144 under the Securities Act, as such Rule may be amended
from time to time, or (b) any similar rule or regulation hereafter adopted by
the SEC. Upon the request of the Investor, the Company will deliver to such
holder a written statement as to whether it has complied with such information
and requirements.

     15.  CONFIDENTIAL INFORMATION. The Investor represents to the Company that,
at all times during the Company's offering of the Shares, the Investor has
maintained in confidence all non-public information regarding the Company
received by the Investor from the Company or its agents, and covenants that it
will continue to maintain in confidence such information until such information
(a) becomes generally publicly available other than through a violation of this
provision by the Investor or its agents or (b) is required to be disclosed in
legal proceedings (such as by deposition, interrogatory, request for documents,
subpoena, civil investigation demand, filing with any governmental authority or
similar process), PROVIDED, HOWEVER, that before making any use or disclosure in
reliance on this subparagraph (b) the Investor shall give the Company at least
fifteen (15) days prior written notice (or such shorter period as required by
law) specifying the circumstances giving rise thereto and will furnish only that
portion of the non-public information which is legally required and will
exercise its reasonable best efforts to obtain reliable assurance that
confidential treatment will be accorded any non-public information so furnished.


                                      -14-