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                                                             EXHIBIT 10.3


                                                           Execution Copy

                          REGISTRATION RIGHTS AGREEMENT

                  This Registration Rights Agreement ("Agreement") dated as of
September 30, 1999, is made between GENOME THERAPEUTICS CORP., a corporation
organized under the laws of the Commonwealth of Massachusetts having its
principal offices at 100 Beaver Street, Waltham, Massachusetts (the "Company"),
and bioMerieux Alliance sa, a societe anonyme organized under the laws of France
having its principal offices at Chemin de l'Orme, 69280 Marcy-l'Etiole, France
("Investor").

                  WHEREAS, Investor desires to purchase, and the Company desires
to issue and sell to Investor 678,610 shares of the Company's Common Stock, $.10
par value per share, upon the terms and conditions set forth in that certain
Common Stock Purchase Agreement dated September 30, 1999 (the "Stock Purchase
Agreement");

                  NOW, THEREFORE, in consideration of the foregoing recitals and
the mutual covenants and agreements herein contained, the parties hereto agree
as follows:

                  1. DEFINITIONS. As used in these provisions, the following
terms shall have the following meanings:

                           "COMMON STOCK" shall mean the common stock, par value
         $.10 per share, of the Company and any other securities into which or
         for which such common stock has been converted or exchanged pursuant to
         a plan of recapitalization, reorganization, merger, sale of assets, or
         otherwise.

                           The terms "REGISTER," "REGISTERED," and
         "REGISTRATION" shall mean a registration effected by the preparation
         and filing of a Registration Statement in compliance with the
         Securities Act, and the declaration or ordering of effectiveness of
         such Registration Statement by the SEC.

                           "REGISTRABLE SECURITIES" shall mean the shares of
         Common Stock beneficially owned by the Investor and all shares of
         common stock issued with respect to, in exchange for, or in replacement
         of such shares of Common Stock. The term "Registrable Securities"
         excludes, however, any security (i) the sale of which has been
         effectively registered under the Securities Act and which has been
         disposed of in accordance with a Registration Statement, (ii) that has
         been sold by the Investor in a transaction exempt from the registration
         and prospectus delivery requirements of the Securities Act under
         Section 4(1) thereof (including, without limitation, transactions
         pursuant to Rules 144 and 144A) such that the further disposition of
         such securities by the transferee or assignee is not restricted under
         the Securities Act, or (iii) that have been sold by the Investor in a
         transaction in which the Investor's rights hereunder are not, or cannot
         be, assigned.


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                           "REGISTRATION EXPENSES" shall mean all expenses
         incident to the Company's performance of or compliance with these
         provisions, including without limitation all (i) registration,
         qualification and filing fees; (ii) fees and expenses of compliance
         with securities or blue sky laws (including reasonable fees and
         disbursements of counsel in connection with blue sky qualifications of
         any Registrable Securities being registered); (iii) printing expenses,
         messenger, telephone and delivery expenses; (iv) internal expenses of
         the Company (including, without limitation, all salaries and expenses
         of employees of the Company performing legal or accounting duties); (v)
         fees and disbursements of counsel for the Company and customary fees
         and expenses for independent certified public accountants retained by
         the Company (including the expenses of any comfort letters or costs
         associated with the delivery by independent certified public
         accountants of comfort letters customarily requested by underwriters);
         (vi) reasonable fees and expenses of one counsel for the Investor;
         (vii) fees and expenses of listing any Registrable Securities on any
         securities exchange on which the shares of Common Stock are then
         listed; and (viii) fees and disbursements of underwriters customarily
         paid by issuers or sellers of securities, but excluding any
         underwriting fees, stock transfer taxes, discounts or commissions
         attributable to the sale of any Registrable Securities and any fees and
         expenses of underwriters' counsel (other than as provided in clause
         (ii) above).

                           "REGISTRATION RIGHTS" shall mean the rights of the
         Investor to cause the Company to register Registrable Securities
         pursuant to Section 2 of this Agreement.

                           "REGISTRATION STATEMENT" shall mean any registration
         statement or similar document that covers any of the Registrable
         Securities pursuant hereto, including the prospectus or preliminary
         prospectus included therein, all amendments and supplements to such
         Registration Statement, including post-effective amendments, all
         exhibits to such Registration Statement and all material incorporated
         by reference in such Registration Statement.

                           "SEC" shall mean the Securities and Exchange
         Commission.

                           "SECURITIES ACT" shall mean the Securities Act of
         1933, as amended, and the rules and regulations promulgated thereunder.

                  2. INCIDENTAL REGISTRATION.

                           (a) If at any time the Company proposes to register
         any of its Common Stock under the Securities Act as an underwritten
         secondary registration on behalf of holders of such securities, the
         Company shall, each such time, give written notice to the Investor of
         its intent to do so; provided, however, that such notification shall
         not be required during the two-year period commencing on the date
         hereof (and the Investor shall have no Registration Rights) unless at
         least one director and/or officer is selling shares in such
         registration. Upon the written request of the Investor given within
         twenty (20) days after mailing of any such


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         notice by the Company, the Company shall, subject to Section 2(b), use
         its best efforts to cause a Registration Statement covering all of the
         Registrable Shares that the Investor has requested to be registered to
         become effective under the Securities Act. The Company shall be under
         no obligation to complete any offering of its securities it proposes to
         make and shall incur no liability to the Investor for its failure to do
         so.

                           (b) If the managing underwriters advise the Company
         in writing that in their opinion the number of securities requested to
         be included in such registration exceeds the number which can be sold
         in an orderly manner in such offering within a price range acceptable
         to the holders initially requesting such registration, the Company will
         include in such registration (i) first, the securities to be included
         in such registration by the Company, (ii) second, the securities
         requested to be included therein by the holders requesting such
         registration, the Registrable Shares requested to be included in such
         registration by the Investor and the securities requested to be
         included therein by holders having piggyback registration rights
         granted by the Company, pro rata among the holders of such securities
         on the basis of the number of securities owned by each such holder, and
         (iii) third, other securities requested to be included in such
         registration.

                  3. REGISTRATION PROCEDURE. Whenever required under these
         provisions to effect the registration of any Registrable Securities,
         the Company shall, as expeditiously as possible:

                           (a) prepare and file with the SEC, as soon as
         practicable, a Registration Statement with respect to such Registrable
         Securities and use its reasonable best efforts to cause such
         Registration Statement to become effective, and keep such Registration
         Statement effective for up to six months or such shorter period as
         shall be required to sell all of the Registrable Securities covered by
         such Registration Statement;

                           (b) prepare and file with the SEC such amendments,
         post-effective amendments and supplements to such Registration
         Statement and the prospectus used in connection with such Registration
         Statement as may be necessary to comply with the provisions of the
         Securities Act with respect to the disposition of all Registrable
         Securities covered by such Registration Statement;

                           (c) furnish to the Investor, without charge, such
         number of copies of a prospectus, including a preliminary prospectus,
         and any amendments or supplements thereto as the Investor may
         reasonably request and a reasonable number of copies of the then-
         effective Registration Statement and any post-effective amendment
         thereto, including financial statements and schedules, all documents
         incorporated therein by reference and all exhibits (including those
         incorporated by reference);

                           (d) promptly after the filing of any document that is
         to be incorporated by reference into a Registration Statement or
         prospectus, provide copies of such document to the Investor and any
         underwriter;


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                           (e) use its reasonable best efforts to register and
         qualify the securities covered by such Registration Statement under
         such other securities or blue sky laws of such jurisdictions as shall
         be reasonably requested by the Investor; provided, however, that the
         Company shall not be required to qualify to do business, file a general
         consent to service of process or subject itself to taxation in any such
         states or jurisdictions where it would not otherwise be required to so
         qualify to do business or consent to service of process or subject
         itself to taxation;

                           (f) cooperate with the Investor and the underwriters
         participating in the disposition of such Registrable Securities and
         their respective counsel in connection with any filings required to be
         made with the National Association of Securities Dealers, Inc.;

                           (g) enter into and perform its obligations under any
         underwriting agreement, in usual and customary form, with the
         underwriter(s) of such offering, in accordance with such terms and
         conditions as the Company and the underwriter(s) may agree. The
         Investor shall also enter into and perform its obligations under such
         an agreement;

                           (h) notify the Investor at any time when a prospectus
         relating thereto is required to be delivered under the Securities Act,
         of the occurrence of any event as a result of which the prospectus
         included in such Registration Statement, as then in effect, includes an
         untrue statement of a material fact or omits to state a material fact
         required to be stated therein or necessary to make the statements
         therein not misleading in the light of the circumstances then existing
         and, at the request of the Investor, the Company will prepare a
         supplement or amendment to such prospectus so that, as thereafter
         delivered to the purchasers of such Registrable Securities, such
         prospectus will not contain an untrue statement of a material fact or
         omit to state any fact necessary to make the statements therein not
         misleading;

                           (i) cause all Registrable Securities covered by the
         Registration Statement to be listed on each securities exchange or
         automated quotation system on which the Company's shares of Common
         Stock are then listed;

                           (j) furnish, at the request of the Investor, on the
         date that such Registrable Securities are delivered to the underwriters
         for sale in connection with a registration pursuant to these
         provisions, (A) an opinion of counsel representing the Company for the
         purposes of such registration, and (B) a letter addressed to the
         underwriters from independent certified public accountants of the
         Company, in each case to be dated such date and to be in form and
         substance as is customarily given by counsel or independent certified
         public accountants, as the case may be, to underwriters in an
         underwritten public offering;

                           (k) permit a representative of the Investor, any
         underwriter participating in any disposition pursuant to such
         registration and any attorney or accountant retained by the Investor or
         underwriter, to participate, at each person's own expense, in the
         preparation



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         of the Registration Statement, and cause the Company's employees to
         supply all information reasonably requested by any such representative,
         underwriter, attorney or accountant in connection with such
         registration; provided, however, that such representatives,
         underwriters, attorneys or accountants shall enter into a
         confidentiality agreement, in form and substance reasonably
         satisfactory to the Company, prior to the release or disclosure of any
         such information; and

                           (l) cooperate with the Investor and the managing
         underwriters to facilitate the timely preparation and delivery of
         certificates representing Registrable Securities to be sold and not
         bearing any restrictive legends, and enable such Registrable Securities
         to be in such denominations and registered in such names as the
         managing underwriters may request at least two (2) business days prior
         to any sale of Registrable Securities to the underwriters.

                  4. RIGHT TO WITHDRAW REGISTRATION. Notwithstanding anything
herein to the contrary, the Company may delay, suspend or withdraw any
registration or qualification of Registrable Securities at any time without
liability or obligation to the Investor.

                  5. OBLIGATION OF THE INVESTOR TO FURNISH INFORMATION. It shall
be a condition precedent to the obligations of the Company to take any action
pursuant to these provisions with respect to any Registrable Securities that the
Investor furnish to the Company such information regarding itself, the
Registrable Securities held by it, and the intended method of disposition of
such Registrable Securities as shall be required to effect the registration of
the Investor's Registrable Securities.

                  The Investor agrees that, upon receipt of any notice from the
Company of the occurrence of any event of the kind described in Section 3(h)
hereof, the Investor shall forthwith discontinue disposition of Registrable
Securities pursuant to the then current prospectus until (i) the Investor is
advised in writing by the Company that a new Registration Statement covering the
reoffer of Registrable Securities has become effective under the Securities Act,
or (ii) the Investor receives copies of a supplemented or amended prospectus
contemplated by Section 3 hereof, or (iii) until the Investor is advised in
writing by the Company that the use of the then current prospectus may be
resumed. The Company shall use its reasonable best efforts to limit the duration
of any discontinuance of disposition of Registrable Securities pursuant to this
paragraph.

                  6. REGISTRATION EXPENSES. In the case of any registration of
Registrable Securities required pursuant to these provisions, the Company shall
pay all Registration Expenses regardless of whether the Registration Statement
becomes effective.

                  7. INDEMNIFICATION AND CONTRIBUTION.

                           (a) INDEMNIFICATION BY THE COMPANY. In the event any
Registrable Securities are included in a Registration Statement pursuant to
these provisions, the Company hereby agrees to indemnify and hold harmless the
Investor, its directors, officers and employees and each



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person, if any, who "controls" (within the meaning of the Securities Act) the
Investor (the "Investor Indemnitees") against all losses, claims, damages, or
liabilities, joint or several, or actions in respect thereof ("Losses") to which
such Investor Indemnitees may become subject under the Securities Act, or
otherwise, insofar as such Losses arise out of, or are based upon, any untrue
statement or alleged untrue statement of any material fact contained in such
Registration Statement, any related preliminary prospectus, or any related
prospectus or any amendment or supplement thereto, or arise out of, or are based
upon, the omission or alleged omission to state therein a material fact required
to be stated therein or necessary to make the statements therein not misleading,
and will reimburse such Investor Indemnitees for any legal or other expenses
reasonably incurred by it or them in connection with investigating or defending
any such Losses; provided, however, that the Company will not be so liable to
the extent that any such Losses arise out of, or are based upon, an untrue
statement or alleged untrue statement of a material fact or an omission or
alleged omission to state a material fact in such Registration Statement, such
preliminary prospectus, or such prospectus, or any such amendment or supplement
thereto in reliance upon, and in conformity with, written information furnished
to the Company by or on behalf of the Investor or an underwriter specifically
for use therein; provided further, that the Company shall not be liable, and
this indemnification agreement shall not apply, to the extent that any such
Losses are solely attributable to the failure of the Investor (or underwriter or
agent acting on its behalf) to deliver a final prospectus (or amendment or
supplement thereto) that corrects a material misstatement or omission contained
in the preliminary prospectus (or final prospectus). The Company hereby agrees
to indemnify underwriters, selling brokers, dealer managers and similar
securities industry professionals participating in the distribution, their
respective officers and directors and each person who "controls" (within the
meaning of the Securities Act) such persons to the same extent as provided above
with respect to the indemnification of the Investor Indemnitees, if so
requested, except with respect to information furnished in writing specifically
for use in any prospectus or Registration Statement by the Investor or any such
underwriters.

                           (b) INDEMNIFICATION BY THE INVESTOR.  With respect to
written information furnished to the Company in connection with any registration
pursuant to the terms of these provisions by or on behalf of the Investor
specifically for use in a Registration Statement, any related preliminary
prospectus, or any related prospectus or any supplement or amendment thereto,
the Investor shall severally indemnify and hold harmless the Company, its
directors, officers and employees and each person, if any, who "controls"
(within the meaning of the Securities Act) the Company (the "Company
Indemnitees") against any Losses to which the Company or such other person
entitled to indemnification hereunder may become subject under the Securities
Act, or otherwise, insofar as such Losses arise out of, or are based upon, any
untrue statement or alleged untrue statement of any material fact contained in
such Registration Statement, such preliminary prospectus, or such prospectus, or
any such amendment or supplement thereto, or arise out of, or are based upon,
the omission or alleged omission to state therein a material fact required to be
stated therein or necessary to make the statements therein not misleading; and
the Investor shall reimburse the Company Indemnitees for any legal or other
expenses reasonably incurred by it or them in connection with investigating or
defending any such Losses, in each case to the extent, but only to the extent,
that the same arises out of, or is based upon, an untrue statement or alleged
untrue statement of a material fact or an omission or alleged omission to state
a material fact in such



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Registration Statement, such preliminary prospectus, or such prospectus or any
such amendment or supplement thereto in reliance upon, and in conformity with,
such written information. In no event shall the liability of the Investor
hereunder be greater in amount than the dollar amount of the proceeds (net of
the payment of all expenses by the Investor) received by the Investor upon the
sale of the Registrable Securities giving rise to such indemnification
obligation. The Company shall be entitled to receive indemnities from
underwriters, selling brokers, dealer managers and similar securities industry
professionals participating in the distribution, to the same extent as provided
above with respect to the information so furnished in writing by such persons
specifically for inclusion in any prospectus or Registration Statement. The
Investor shall also indemnify underwriters, selling brokers, dealer managers and
similar securities industry professionals participating in the distribution,
their officers and directors and each person who "controls" (within the meaning
of the Securities Act) such persons to the same extent as provided above with
respect to the indemnification of the Company, if so requested.

                           (c) CONDUCT OF INDEMNIFICATION PROCEEDINGS.  Promptly
after receipt by an indemnified party hereunder of notice of any claim or the
commencement of any action by a claimant not an indemnified party hereunder
("Third-Party Claim"), the indemnified party shall, if a claim for
indemnification in respect thereof is to be made by such indemnified party
against an indemnifying party, promptly notify such indemnifying party in
writing of such Third-Party Claim as soon as is reasonably practicable after
said claim is actually known to the indemnified party; provided, however, that
the right of an indemnified party to be indemnified hereunder in respect of
Third-Party Claims shall not be adversely affected by such indemnified party's
failure to notify the indemnifying party of such Third-Party Claim unless, and
then only to the extent that, an indemnifying party is actually damaged or
suffers any loss or incurs any additional expense as a result thereof. If any
such Third-Party Claim is brought against an indemnified party, and it promptly
notifies the indemnifying party thereof, the indemnifying party shall be
entitled to assume the defense thereof with counsel selected by the indemnifying
party and reasonably satisfactory to the indemnified party. After the
indemnifying party gives notice to the indemnified party of its election to
assume the defense of such Third-Party Claim, (i) the indemnifying party shall
not, except as provided below, be liable to the indemnified party for any legal
or other expense subsequently incurred by the indemnified party in connection
with the defense thereof, (ii) the indemnifying party shall not be liable for
the costs and expenses of any settlement of such claim or action unless such
settlement was effected with the written consent of the indemnifying party or
the indemnified party waived any rights to indemnification hereunder in writing,
in which case the indemnified party may effect a settlement without such consent
at its own cost and expense, and (iii) the indemnified party shall be obligated
to cooperate with the indemnifying party in the investigation of such claim or
action; provided, however, that the Investor Indemnitees may employ their own
counsel to participate in the defense of a Third-Party Claim if they have been
advised by counsel in writing that, in the reasonable judgment of such counsel,
it is advisable for such Investor Indemnitees to be represented by separate
counsel due to the presence of a conflict of interest between such Investor
Indemnitees and the indemnifying party, and in such event the fees and expenses
of such separate counsel shall be paid by the Company; provided further, that
the Company shall not be liable for the reasonable fees and expenses of more
than one separate counsel at any time for all such Investor Indemnitees. An
indemnifying party shall not, without the prior written consent



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of the indemnified parties, settle, compromise or consent to the entry of any
judgment with respect to any pending or threatened Third-Party Claim in respect
of which indemnification or contribution may be sought hereunder (whether or not
the indemnified parties are actual or potential parties to such Third-Party
Claim) unless such settlement, compromise or consent includes a release of such
indemnified party reasonably acceptable to such indemnified party from all
liability arising out of such Third-Party Claim, or unless the indemnifying
party shall confirm in a written agreement reasonably acceptable to such
indemnified party that, notwithstanding any federal, state or common law, such
settlement, compromise or consent shall not adversely affect the right of any
indemnified party to indemnification or contribution as provided in these
provisions.

                           (d) CONTRIBUTION. If for any reason the
indemnification provided for in Sections 7(a) or (b) hereof is unavailable to an
indemnified party or is insufficient to hold it harmless as contemplated
therein, then the indemnifying party shall contribute to the amount paid or
payable by the indemnified party as a result of such loss, claim, damage or
liability in such proportion as is appropriate to reflect not only the relative
benefits received by the indemnifying party and the indemnified party, but also
the relative fault of the indemnifying party and the indemnified party, as well
as any other relevant equitable considerations. 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.

                           (e) SURVIVAL OF INDEMNIFICATION. The obligations
under this Section 7 shall survive the completion of any offering of Registrable
Securities in a Registration Statement pursuant to these provisions, and
otherwise.

                  8. ASSIGNMENT OF REGISTRATION RIGHTS. Neither this Agreement
nor any of the rights and obligations contained herein may be assigned or
otherwise transferred by either party without the written consent of the other
party.

                  9. LIMITATIONS ON SUBSEQUENT REGISTRATION RIGHTS. From and
after the date of these provisions, the Company shall not, without the prior
written consent of the Investor, enter into any agreement, understanding or
other arrangement with any holder or prospective holder of any securities of the
Company which would allow such holder or prospective holder to require the
Company to effect a registration, unless under the terms of such agreement, the
rights of such holder or prospective holder to participate in such registration
shall permit registration on no greater basis than that of the Investor.

                  10. AMENDMENT OF REGISTRATION RIGHTS. Any provision of this
Agreement may be amended or the observance thereof may be waived (either
generally or in a particular instance and either retroactively or
prospectively), only with the written consent of the Company and the Investor.

                  11. NOTICES. Any consent, notice or report required or
permitted to be given or made under this Agreement by one of the parties hereto
to the other shall be in writing, delivered personally or by facsimile (and
promptly confirmed by telephone, personal delivery or courier) or courier,
postage prepaid (where applicable), addressed to such other party at its address
indicated



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below, or to such other address as the addressee shall have last furnished in
writing to the addresser and shall be effective upon receipt by the addressee.


         If to the Company:         Genome Therapeutics Corp.
                                    100 Beaver Street
                                    Waltham, MA
                                    Attention: Chief Executive Officer
                                    Telephone: (781) 398-2300
                                    Telecopy: (781) 893-8277

         with a copy to:            Ropes & Gray
                                    One International Place
                                    Boston, Massachusetts 02110
                                    Attention:  David C. Chapin, Esq.
                                    Telephone:  (617) 951-7000
                                    Telecopy:  (617) 951-7050

         If to Investor:            bioMerieux Alliance sa
                                    Chemin de l'Orme
                                    69280 Marcy-l'Etiole
                                    France
                                    Attention:  Paul Caroly

                                    Telephone:  33-4-7887-2000
                                    Telecopy:  33-4-7887-5370

         with a copy to:            Bryan Cave LLP
                                    211 North Broadway, Suite 3600
                                    St. Louis, Missouri 63102-2750
                                    Attention:  James L. Nouss, Jr., Esq.

                                    Telephone:  (314) 259-2000
                                    Telecopy:  (314) 259-2020

                  12. GOVERNING LAW. This Agreement shall be governed by and
construed in accordance with the laws of the Commonwealth of Massachusetts,
excluding choice-of-law principles of the law of such Commonwealth that would
require the application of the laws of a jurisdiction other than such
Commonwealth.


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                  IN WITNESS WHEREOF, the parties have executed this Agreement
on the day and year first above written.

                                       BIOMERIEUX ALLIANCE sa

                                       By:      ___________________________
                                       Name:    ___________________________
                                       Title:   ___________________________

                                       GENOME THERAPEUTICS CORP.

                                       By:      ___________________________
                                       Name:    ___________________________
                                       Title:   ___________________________




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