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                                                                    Exhibit 4.5

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AS AMENDED, OR REGISTERED OR QUALIFIED UNDER ANY
STATE SECURITIES LAWS. THE SECURITIES MAY NOT BE SOLD, TRANSFERRED, PLEDGED OR
HYPOTHECATED UNLESS SUCH SALE, TRANSFER, PLEDGE OR HYPOTHECATION IS IN
ACCORDANCE WITH SUCH ACT AND APPLICABLE STATE SECURITIES LAWS.

                                     WARRANT

                           TO PURCHASE COMMON STOCK OF

                        GENAISSANCE PHARMACEUTICALS, INC.

         THIS WARRANT IS TO CERTIFY THAT RITCHIE LONG/SHORT TRADING LTD., a
Cayman Islands exempted company, is entitled to purchase from Genaissance
Pharmaceuticals, Inc., a Delaware corporation (the "COMPANY"), 261,500 shares of
Common Stock, par value $0.001 per share, of the Company (the "COMMON STOCK")
for the Exercise Price described herein upon the terms and conditions set forth
herein.

         Section 1. CERTAIN DEFINITIONS. As used in this Warrant, capitalized
terms used herein shall have the following meanings:

         "AFFILIATE" shall mean, with respect to any particular Person, any
other Person that directly or indirectly controls, is controlled by or is under
common control with such particular Person. For the purpose of this definition,
"CONTROL" means the possession, directly or indirectly, of the power to direct
the management and policies of a Person, whether through the ownership of voting
securities, by contract or otherwise.

         "BUSINESS DAY" shall mean any day except a Saturday, Sunday or other
day on which banks in Chicago, Illinois are authorized or obligated by law or
executive order to close.

         "CLOSING BID PRICE" shall mean, for any security as of any date, the
last closing bid price for such security on the Principal Market as reported by
Bloomberg Financial Markets ("BLOOMBERG"), or, if the Principal Market begins to
operate on an extended hours basis and does not designate the closing bid price,
then the last bid price of such security at 4:00 p.m. New York Time (or such
other time as the Principal Market publicly announces is the official close of
trading) as reported by Bloomberg, or, if the foregoing do not apply, the last
closing bid price of such security in the over-the-counter market on the
electronic bulletin board for such security as reported by Bloomberg, or, if no
closing bid price is reported for such security by Bloomberg, the last closing
trade price for such security as reported by Bloomberg, or, if no last closing
trade price is reported for such security by Bloomberg, the average of the bid
prices of any market makers for such security as reported in the "pink sheets"
by the National Quotation Bureau, Inc. If the Closing Bid Price cannot be
calculated for such security on such date on any of the foregoing bases, the
Closing Bid Price of such security on such date shall be the fair market value
as mutually determined by the Company and the Warrantholders representing a
majority of the Warrant Shares issuable upon exercise of the Warrants then
outstanding. All such determinations will be appropriately adjusted for any
stock dividend, stock split or other similar transaction during such period.

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         "EXPIRATION DATE" shall mean June 30, 2009.

         "LIEN" shall mean any mortgage, pledge, security interest, encumbrance,
lien, claim or charge of any kind.

         "PERSON" shall mean an individual, a partnership, a corporation, a
limited liability company, an association, a joint stock company, a trust, a
joint venture, an unincorporated organization or any other entity.

         "PRINCIPAL MARKET" shall mean the NASDAQ National Market, or if the
Common Stock is not traded on the NASDAQ National Market, then the principal
securities exchange or trading market for the Common Stock.

         "SECURITIES ACT" shall mean the Securities Act of 1933, as amended.

         "WARRANT" shall mean this Warrant and any warrant(s) issued in
substitution for this Warrant.

         "WARRANTHOLDER" shall mean Ritchie Long/Short Trading Ltd., as the
initial holder of this Warrant, and any Affiliate of Ritchie Long/Short Trading
Ltd. to whom this Warrant has been transferred in accordance with Section 10
hereof.

         Section 2. WARRANT SHARES; EXERCISE PRICE.

         (a) This Warrant may be exercised in accordance with SECTION 3 for
261,500 shares of Common Stock (such shares, as may be adjusted from time to
time pursuant to SECTION 4, are referred to herein as the "WARRANT Shares").

         (b) The exercise price for each Warrant Share is $4.17 (such price, as
may be adjusted from time to time pursuant to SECTION 4, is referred to herein
as the "EXERCISE PRICE").

         Section 3. EXERCISE OF WARRANT.

         (a) Subject to SECTION 3(b), the Warrantholder may exercise this
Warrant, in whole, but not in part, at any time beginning on the date hereof
until and including the Expiration Date; provided, however, that in no event
shall the Warrantholder be entitled to exercise this Warrant for a number of
Warrant Shares in excess of that number of Warrant Shares which, upon giving
effect to such exercise, would cause the aggregate number of shares of Common
Stock beneficially owned by the Warrantholder and its Affiliates to exceed 9.99%
of the outstanding shares of the Common Stock following such exercise. For
purposes of the foregoing proviso, the aggregate number of shares of Common
Stock beneficially owned by the Warrantholder and its Affiliates shall include
the number of shares of Common Stock issuable upon exercise of this Warrant with
respect to which the determination of such proviso is being made, but shall
exclude shares of Common Stock which would be issuable upon (i) exercise of the
remaining, unexercised Warrants beneficially owned by the Warrantholder and its
Affiliates and (ii) exercise or conversion of the unexercised or unconverted
portion of any other securities of the Company beneficially owned by the
Warrantholder and its Affiliates (including, without limitation, any convertible
notes or preferred stock) subject to a limitation on conversion or exercise
analogous

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to the limitation contained herein. Except as set forth in the preceding
sentence, for purposes of this paragraph, beneficial ownership shall be
calculated in accordance with Section 13(d) of the Securities Exchange Act of
1934, as amended (the "Exchange Act"). For purposes of this Warrant, in
determining the number of outstanding shares of Common Stock a Warrantholder may
rely on the number of outstanding shares of Common Stock as reflected in (1) the
Company's most recent Quarterly Report on Form 10-Q or Annual Report on Form
10-K, as the case may be, (2) a more recent public announcement by the Company
or (3) any other notice by the Company or its transfer agent setting forth the
number of shares of Common Stock outstanding. Upon the written request of any
Warrantholder, the Company shall promptly, but in no event later than one (1)
Business Day following the receipt of such notice, confirm in writing to any
such Warrantholder the number of shares of Common Stock then outstanding. In any
case, the number of outstanding shares of Common Stock shall be determined after
giving effect to the conversion or exercise of securities of the Company by such
Warrantholder and its Affiliates since the date as of which such number of
outstanding shares of Common Stock was reported.

         (b) The Warrantholder shall exercise this Warrant by delivering to the
Company at the address set forth on the signature page hereto (i) the Exercise
Notice set out at the end of this Warrant, (ii) this Warrant and (iii) subject
to Section 3(g), a cash payment equal to the aggregate Exercise Price by wire
transfer to an account of the Company designated in writing by the Company to
the Warrantholder.

         (c) Upon exercise of this Warrant and delivery of the Exercise Notice
with proper payment relating thereto, the Company shall issue and deliver as
soon as practicable (and in any case within four (4) Business Days thereafter)
to the Warrantholder a stock certificate or certificates, duly executed by the
Company, representing the Warrant Shares.

         (d) The stock certificate or certificates for the Warrant Shares to be
delivered in accordance with this SECTION 3 shall be registered in the name of
the Warrantholder or such other Person as shall be designated in the Exercise
Notice. Such certificate or certificates shall be deemed to have been issued and
the Warrantholder or any other Person so designated to be named therein shall be
deemed to have become the holder of record of such shares, including to the
extent permitted by law the right to vote such shares or to consent or to
receive notice as stockholders, as of the time said notice is delivered to the
Company as aforesaid.

         (e) The Company shall pay all expenses payable in connection with the
preparation, issue and delivery of stock certificates under this SECTION 3,
including any transfer taxes resulting from the exercise of this Warrant by the
Warrantholder and the issuance of the Warrant Shares to the Warrantholder
hereunder.

         (f) Upon the exercise of this Warrant in accordance with the terms
hereof, the Warrant Shares shall be validly issued, fully paid and
non-assessable, and free from all Liens, other than Liens created by the
Warrantholder.

         (g) The Warrantholder may, at its election exercised in its sole
discretion, exercise this Warrant in whole, but not in part, and, in lieu of
making the cash payment otherwise contemplated to be made to the Company upon
such exercise in payment of the aggregate

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Exercise Price, elect instead to receive upon such exercise the "Net Number" of
shares of Common Stock determined according to the following formula (a
"CASHLESS EXERCISE"):

         Net Number = (A X B) - (A X C)
                      -----------------
                              B
                For purposes of the foregoing formula:

                           A= the total number of shares with respect to which
                           this Warrant is then being exercised.

                           B= the Closing Bid Price of the Common Stock on the
                           trading day immediately preceding the date of the
                           Exercise Notice.

                           C= the Exercise Price then in effect for the
                           applicable Warrant Shares at the time of such
                           exercise.

         Section 4. ADJUSTMENT OF EXERCISE PRICE AND WARRANT SHARES.

         (a) If, at any time prior to the Expiration Date, the number of
outstanding shares of Common Stock is (i) increased by a stock dividend payable
in shares of Common Stock or by a subdivision or split-up of shares of Common
Stock or (ii) decreased by a combination of shares of Common Stock, then,
following the record date fixed for the determination of holders of Common Stock
entitled to receive the benefits of such stock dividend, subdivision, split-up,
or combination, the Exercise Price shall be adjusted to a new amount equal to
the product of (I) the Exercise Price in effect on such record date and (II) the
quotient obtained by dividing (x) the number of shares of Common Stock
outstanding on such record date (without giving effect to the event referred to
in the foregoing clause (i) or (ii)), by (y) the number of shares of Common
Stock which would be outstanding immediately after the event referred to in the
foregoing clause (i) or (ii), if such event had occurred immediately following
such record date.

         (b) Upon each adjustment of the Exercise Price as provided in SECTION
4(a), the Warrantholder shall thereafter be entitled to purchase, at the
Exercise Price resulting from such adjustment, the number of shares of Common
Stock equal to the product of (i) the number of shares of Common Stock that the
Warrantholder was entitled to purchase prior to such adjustment and (ii) the
quotient obtained by dividing (x) the Exercise Price existing prior to such
adjustment by (y) the new Exercise Price resulting from such adjustment.

         Section 5. RECLASSIFICATION, ETC. In case of any reclassification or
change of the outstanding shares of Common Stock (other than as a result of a
subdivision, combination or stock dividend), or in case of any consolidation of
the Company with, or merger of the Company into, another corporation or other
business organization (other than a consolidation or merger in which the Company
is the continuing corporation and which does not result in any reclassification
or material change of the outstanding shares of Common Stock) at any time prior
to the Expiration Date, then, as a condition of such reclassification,
reorganization, change, consolidation or merger, lawful provision shall be made,
and duly executed documents

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evidencing the same from the Company or its successor shall be delivered to the
Warrantholder, so that the Warrantholder shall have the right prior to the
Expiration Date to purchase, at a price not to exceed the aggregate Exercise
Price, the kind and amount of shares of stock and other securities and property
receivable upon such reclassification, reorganization, change, consolidation or
merger by a holder of the number of shares of Common Stock purchasable by the
Warrantholder immediately prior to such reclassification, reorganization,
change, consolidation or merger, and in any such case appropriate provisions
shall be made with respect to the rights and interest of the Warrantholder to
the end that the provisions hereof shall thereafter be applicable in relation to
any shares of stock and other securities and property thereafter deliverable
upon exercise hereof.

         Section 6. RESERVATION AND AUTHORIZATION OF COMMON STOCK. The Company
shall at all times reserve and keep available for issuance such number of its
authorized but unissued shares of Common Stock as will be sufficient to permit
the exercise of this Warrant.

         Section 7. STOCK BOOKS. The Company will not at any time, except upon
dissolution, liquidation or winding up or in accordance with SECTION 5, close
its stock books so as to result in preventing or delaying the exercise of this
Warrant during normal business hours.

         Section 8. LIMITATION OF LIABILITY. No provisions hereof, in the
absence of affirmative action by the Warrantholder to purchase the Warrant
Shares hereunder, shall give rise to any liability of the Warrantholder to pay
the Exercise Price or as a stockholder of the Company (whether such liability is
asserted by the Company or creditors of the Company).

         Section 9. LEGEND. Each stock certificate representing Warrant Shares
shall bear a legend substantially in the following form:

         "THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN
REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE "ACT"), OR UNDER
APPLICABLE STATE SECURITIES LAWS, AND MAY NOT BE SOLD, ASSIGNED, PLEDGED OR
OTHERWISE TRANSFERRED EXCEPT PURSUANT TO AN EFFECTIVE REGISTRATION UNDER THE ACT
OR IN A TRANSACTION WHICH QUALIFIES AS AN EXEMPT TRANSACTION UNDER THE ACT, THE
RULES AND REGULATIONS PROMULGATED THEREUNDER AND THE SECURITIES LAW OF ANY
APPLICABLE STATE."

         Section 10. TRANSFER. Subject to compliance with the Securities Act and
the applicable rules and regulations promulgated thereunder, the Warrantholder
may transfer this Warrant, in whole, but not in part, to any of its Affiliates
without the consent of the Company. Any such transfer shall be made at the
office or agency of the Company at which this Warrant is exercisable, by the
registered holder hereof in person or by its duly authorized attorney, upon
surrender of this Warrant together with the assignment hereof properly endorsed,
and promptly thereafter a new warrant shall be issued and delivered by the
Company, registered in the name of the assignee. Until registration of transfer
hereof on the books of the Company, the Company may treat the Warrantholder as
the owner hereof for all purposes.

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         Section 11. REPRESENTATIONS, WARRANTIES AND COVENANTS AS TO COMMON
STOCK. The Company hereby represents, warrants, covenants and agrees as follows:

         (a) This Warrant is, and any Warrants issued in substitution for or
replacement of this Warrant will upon issuance be, duly authorized and validly
issued, and no further consent or authorization is required by the Company, its
Board of Directors or its stockholders. The Company has the requisite corporate
power and authority to enter into and perform its obligations under this Warrant
and to issue the Warrant Shares in accordance with the terms hereof. This
Warrant constitutes the valid and binding obligation of the Company, enforceable
against the Company in accordance with its terms.

         (b) All Warrant Shares which may be issued upon the exercise of the
rights represented by this Warrant will, upon issuance, be validly issued, fully
paid and nonassessable and free from all taxes, liens and charges imposed by the
Company with respect to the issuance thereof.

         (c) During the period within which the rights represented by this
Warrant may be exercised, the Company will at all times have authorized and
reserved at least 100% of the number of shares of Common Stock needed to provide
for the exercise of the rights then represented by this Warrant, and the par
value of said shares will at all times be less than or equal to the applicable
Exercise Price.

         (d) Subject to Section 5 hereof, the Company will not, by amendment of
its Amended and Restated Certificate of Incorporation, as amended (the
"Certificate of Incorporation"), or through any reorganization, transfer of
assets, consolidation, merger, dissolution, issue or sale of securities, or any
other voluntary action, avoid or seek to avoid the observance or performance of
any of the terms to be observed or performed by it hereunder, but will at all
times in good faith assist in the carrying out of all the provisions of this
Warrant consistent with the tenor, purpose and specific language of this
Warrant. Without limiting the generality of the foregoing, the Company (i) will
not increase the par value of any shares of Common Stock receivable upon the
exercise of this Warrant above the Exercise Price then in effect, and (ii) will
take all such actions as may be necessary or appropriate in order that the
Company may validly and legally issue fully paid and nonassessable shares of
Common Stock upon the exercise of this Warrant.

         (e) The execution, delivery and performance of this Warrant by the
Company, the performance by the Company of its obligations hereunder and the
consummation by the Company of the transactions contemplated hereby (including,
without limitation, the reservation for issuance and issuance of the Warrant
Shares) will not (i) result in a violation of the Certificate of Incorporation,
any certificate of designations, preferences and rights of any outstanding
series of preferred stock of the Company or its bylaws; (ii) conflict with, or
constitute a default (or an event which with notice or lapse of time or both
would become a default) under, or give to others any rights of termination,
amendment, acceleration or cancellation of, any material agreement, indenture or
instrument to which the Company or any of its subsidiaries is a party other than
any of the foregoing events listed in this clause (ii) which do not individually
or in the aggregate have a material adverse effect on the Company; (iii) result
in a violation of any law, rule, regulation, order or judgment (including,
without limitation, federal

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and state securities laws and regulations and the rules and regulations of the
Principal Market) applicable to the Company or any of its subsidiaries or by
which any property or assets of the Company or any of its subsidiaries is bound.

         (f) Subject to the filing of an additional listing application with the
NASDAQ National Market, the Company is not required to obtain any consent,
authorization or order of, or make any filing or registration with, any court or
governmental agency or any regulatory or self-regulatory agency in order for it
to execute, deliver or perform any of its obligations under this Warrant.

         (g) Subject to Section 5 hereof, this Warrant will be binding upon any
entity succeeding to the Company by merger, consolidation or acquisition of all
or substantially all of the Company's assets.

         Section 12. LOSS, DESTRUCTION, ETC. OF WARRANT. Upon receipt of
evidence reasonably satisfactory to the Company of the loss, theft, destruction
or mutilation of this Warrant and, in the case of any such mutilation, upon
surrender and cancellation of this Warrant, the Company will make and deliver,
in lieu of such lost, stolen, destroyed or mutilated Warrant, a new warrant of
like tenor and representing the right to purchase the Warrant Shares.

         Section 13. AMENDMENTS. Any term of this Warrant may be amended or
waived (either generally or in a particular instance and either retroactively or
prospectively) with the written consent of the Company and the Warrantholders
representing at least a majority of the number of Warrant Shares then subject to
this Warrant or any warrant issued pursuant to Section 10 hereof. No waivers of
any term, condition or provision of this Warrant, in any one or more instances,
shall be deemed to be, or construed as, a further or continuing waiver of any
such term, condition or provision.

         Section 14. NOTICES. All notices or other communications required or
permitted hereunder shall be in writing and shall be deemed given or delivered
(a) when delivered personally, (b) if transmitted by facsimile when confirmation
of transmission is received, (c) if sent by registered or certified mail,
postage prepaid, return receipt requested, three Business Days after mailing or
(d) if sent by reputable overnight courier service, one Business Day after
delivery to such service; and shall be addressed as follows:

IF TO THE COMPANY, TO:                WITH A COPY TO:
---------------------                 --------------

Genaissance Pharmaceuticals, Inc.     Wilmer Cutler Pickering Hale and Dorr LLP
Five Science Park                     60 State Street
New Haven, Connecticut 06511          Boston, Massachusetts 02109
Attention: Chief Financial Officer    Attention: Steven D. Singer, Esq.
Facsimile: (203) 786-3567             Facsimile: (617) 526-5000

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IF TO THE WARRANTHOLDER, TO:          WITH A COPY TO:
---------------------------           --------------

Ritchie Long/Short Trading Ltd.       Katten Muchin Zavis Rosenman
c/o Ritchie Capital Management, LLC   525 West Monroe Street, Suite 1600
2100 Enterprise Avenue                Chicago, Illinois 60661
Geneva, Illinois 60134                Attention: Mark D. Wood, Esq.
Attention: Jim Park                   Facsimile: (312) 902-1061
Facsimile: (630) 761-0100

         Section 15. SUCCESSORS AND ASSIGNS. This Warrant shall bind and inure
to the benefit of and be enforceable by the parties hereto and their respective
permitted successors and assigns.

         Section 16. INDEMNIFICATION.

         (a) To the fullest extent permitted by law, the Company will, and
hereby does, indemnify, hold harmless and defend each Warrantholder, the
directors, officers, partners, employees, agents, representatives of, and each
person, if any, who controls any Warrantholder within the meaning of the
Securities Act or the Exchange Act (each, an "INDEMNIFIED PERSON"), from and
against any and all actions, causes of action, suits, claims, losses, costs,
penalties, fees, liabilities and damages, and expenses in connection therewith
(irrespective of whether any such Indemnified Person is a party to the action
for which indemnification hereunder is sought), and including reasonable
attorneys' fees and disbursements (the "INDEMNIFIED LIABILITIES"), incurred by
any Indemnified Person as a result of, or arising out of, or relating to: (i)
any misrepresentation or breach of any representation or warranty or breach of
any covenant, agreement or obligation made by the Company in this Warrant or any
other certificate, instrument or document contemplated hereby, (ii) in the event
any Warrant Shares are registered in any registration statement of the Company,
any untrue statement or alleged untrue statement of a material fact contained in
such registration statement or any post-effective amendment thereto, or the
omission or alleged omission to state a material fact required to be stated
therein or necessary to make the statements therein not misleading, (iii) in the
event any Warrant Shares are registered in any registration statement of the
Company, any untrue statement or alleged untrue statement of a material fact
contained in any preliminary prospectus if used prior to the effective date of
such registration statement, or contained in the final prospectus (as amended or
supplemented, if the Company files any amendment thereof or supplement thereto
with the Securities and Exchange Commission) or the omission or alleged omission
to state therein any material fact necessary to make the statements made therein
not misleading in light of the circumstances in which they were made, or (iv) in
the event any Warrant Shares are registered in any registration statement of the
Company, any violation or alleged violation by the Company of the Securities
Act, the Exchange Act, any state securities law, or any rule or regulation
thereunder relating to the offer or sale of the Warrant Shares pursuant to such
registration statement (the matters in the foregoing clauses (i) through (iv)
being, collectively, "Violations"). Notwithstanding anything to the contrary
contained herein, the indemnification agreement contained in this Section 16(a)
shall not apply to an Indemnified Liability by an Indemnified Person arising out
of or based upon a Violation which occurs in reliance upon and in conformity
with information furnished in writing to the Company by such Indemnified Person
for such Indemnified Person expressly for use in connection with the preparation
of a registration

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statement or any such amendment thereof or supplement thereto. Such indemnity
shall remain in full force and effect regardless of any investigation made by or
on behalf of the Indemnified Person and shall survive the transfer of the
Warrant Shares by the Warrantholders pursuant to Section 10.

         (b) To the fullest extent permitted by law, each Warrantholder,
severally and not jointly, will, and hereby does, indemnify, hold harmless and
defend the Company, each of its directors, each of its officers who signs the
registration statement and each person, if any, who controls the Company within
the meaning of the Securities Act or the Exchange Act (each, a "COMPANY
INDEMNIFIED PERSON"), from and against any and all actions, causes of action,
suits, claims, losses, costs, penalties, fees, liabilities and damages, and
expenses in connection therewith (irrespective of whether any such Company
Indemnified Person is a party to the action for which indemnification hereunder
is sought), and including reasonable attorneys' fees and disbursements (the
"COMPANY INDEMNIFIED LIABILITIES"), incurred by any Company Indemnified Person
as a result of, or arising out of, or relating to, (i) in the event any Warrant
Shares are registered in any registration statement of the Company, any untrue
statement or alleged untrue statement of a material fact contained in such
registration statement or any post-effective amendment thereto, or the omission
or alleged omission to state a material fact required to be stated therein or
necessary to make the statements therein not misleading, or (ii) in the event
any Warrant Shares are registered in any registration statement of the Company,
any untrue statement or alleged untrue statement of a material fact contained in
any preliminary prospectus if used prior to the effective date of such
registration statement, or contained in the final prospectus (as amended or
supplemented, if the Company files any amendment thereof or supplement thereto
with the Securities and Exchange Commission) or the omission or alleged omission
to state therein any material fact necessary to make the statements made therein
not misleading in light of the circumstances in which they were made (the
matters in the foregoing clauses (i) and (ii) being, collectively, "OTHER
VIOLATIONS"), if and to the extent (and only to the extent) such Other
Violations were made in reliance upon and in conformity with information
relating to such Warrantholder furnished in writing to the Company by such
Warrantholder specifically for use in connection with the preparation of such
registration statement or any such amendment thereof or supplement thereto;
provided, however, that the Warrantholder shall be liable under this Section
16(b) for only that amount of a Company Indemnified Liability as does not exceed
the net proceeds to such Warrantholder as a result of the sale of Warrant Shares
pursuant to such registration statement giving rise to such Company Indemnified
Liability. Such indemnity shall remain in full force and effect regardless of
any investigation made by or on behalf of the Company Indemnified Person and
shall survive the transfer of the Warrant Shares by the Warrantholders pursuant
to Section 10.

         (c) The indemnification required by this Section 16 shall be made by
periodic payments of the amount thereof during the course of the investigation
or defense, as and when bills are received or Indemnified Liabilities or Company
Indemnified Liabilities are incurred.

         (d) To the extent any indemnification by an indemnifying party is
prohibited or limited by law, the indemnifying party agrees to make the maximum
contribution with respect to any amounts for which it would otherwise be liable
under Section 16 to the fullest extent permitted by law, in such proportion as
is appropriate to reflect the relative fault of the Company on the one hand and
the Warrantholder on the other in connection with the statements or

                                      -9-
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omissions which resulted in any Indemnified Liabilities or Company Indemnified
Liabilities, as well as any other relevant equitable considerations. The
relative fault of the Company and the Warrantholder shall be determined by
reference to, among other things, whether the untrue or alleged untrue statement
of material fact related to information supplied by the Company or the
Warrantholder and the parties' relative intent, knowledge, access to information
and opportunity to correct or prevent such statement or omission. The Company
and the Warrantholder agree that it would not be just and equitable if
contribution pursuant to this Section 16(d) were determined by pro rata
allocation or by any other method of allocation which does not take account of
the equitable considerations referred to above. 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) Any party entitled to contribution or indemnification under this
Section 16 will, promptly after receipt of notice of commencement of any action,
suit or proceeding against such party in respect of which a claim for
contribution or indemnification may be made against another party or parties
under this Section 16, notify such party or parties from whom contribution or
indemnification may be sought, but the omission so to notify such party or
parties from whom contribution or indemnification may be sought shall not
relieve such party from any other obligation it or they may have thereunder or
otherwise under this Section 16. No party shall be liable for contribution or
indemnification with respect to any action, suit, proceeding or claim settled
without its prior written consent, which consent shall not be unreasonably
withheld, conditioned or delayed. No indemnifying party shall, without the prior
written consent of the Indemnified Person or Company Indemnified Person, consent
to entry of any judgment or enter into any settlement or other compromise which
does not include as an unconditional term thereof the giving by the claimant or
plaintiff to such Indemnified Person or Company Indemnified Person of a release
from all liability in respect to such claim or litigation.

         Section 17. GOVERNING LAW. This Warrant and the obligations arising
hereunder shall be governed by, and construed and enforced in accordance with,
the laws of the State of Delaware (other than its conflicts of law provisions).

         Section 18. NO STOCKHOLDER RIGHTS WITH RESPECT TO WARRANT SHARES. Until
the Warrant Shares subject to this Warrant are issued to the Warrantholder upon
exercise of this Warrant, the Warrantholder shall have no right to vote the
Warrant Shares in connection with any matters to which holders of Common Stock
are entitled to vote and shall have no rights as a stockholder of the Company
with respect to the Warrant Shares.

                            [SIGNATURE PAGE FOLLOWS]

                                      -10-
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         IN WITNESS WHEREOF, the Company has caused this Warrant to be executed
by a duly authorized officer as of June 30, 2004.

                                  GENAISSANCE PHARMACEUTICALS, INC.,
                                  a Delaware corporation

                                  By: /s/ BEN D. KAPLAN
                                      -----------------------------------------
                                      Name:  Ben D. Kaplan
                                      Title: Senior Vice President & CFO

                                  Address:

                                  Five Science Park
                                  New Haven, Connecticut 06511
                                  Attention: Chief Financial Officer
                                  Fax: (203) 786-3567

AGREED AND ACKNOWLEDGED
AS OF JUNE 30, 2004:

RITCHIE LONG/SHORT TRADING LTD.,
a Cayman Islands exempted company

By: /s/ JIM PARK
    --------------------------------------------
    Name:  Jim Park
    Title: Authorized Signatory

                                 SIGNATURE PAGE
                                     TO THAT
                                     WARRANT

<Page>

                                 EXERCISE NOTICE

                 (to be executed only upon exercise of Warrant)

To: Genaissance Pharmaceuticals, Inc.
    Five Science Park
    New Haven, Connecticut 06511
    Attention: Chief Financial Officer

         The undersigned, pursuant to the provisions set forth in the attached
Warrant, hereby irrevocably elects to purchase all of the Warrant Shares covered
by such Warrant and herewith [makes payment] or [elects to make a Cashless
Exercise] of the aggregate Exercise Price as provided for in such Warrant.

         The Warrant Shares shall be registered in the name of the following
Person:

----------------------------------.

         Dated:                            Name:
               -------------------               ------------------------------

                                           Signature:
                                                     --------------------------

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

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

                                                   ----------------------------<Page>

                                                                  Exhibit 10.50

                         Ritchie Capital Management, LLC
                             2100 Enterprise Avenue
                             Geneva, Illinois 60134

                                  June 29, 2004

Genaissance Pharmaceuticals, Inc.
Five Science Park
New Haven, Connecticut 06511

Attn: Kevin Rakin

         Re:  LIMITATIONS ON CONVERSIONS

Dear Mr. Rakin:

         Reference is made to that certain Securities Purchase Agreement, dated
as of October 29, 2003, by and between Genaissance Pharmaceuticals, Inc. (the
"COMPANY") and RAM Trading, Ltd. (the "SECURITIES PURCHASE AGREEMENT"), the
Registration Rights Agreement, dated as of October 29, 2003, by and between the
Company and RAM Trading, Ltd. (the "REGISTRATION RIGHTS AGREEMENT"), the
Certificate of Designations, Preferences and Rights of the Series A Preferred
Stock of the Company (the "CERTIFICATE OF DESIGNATIONS") and the warrants (the
"WARRANTS") to purchase shares of the Company's Series A Preferred Stock issued
pursuant to the Securities Purchase Agreement (the Securities Purchase
Agreement, the Registration Rights Agreement, the Warrants and the Certificate
of Designations, collectively the "TRANSACTION DOCUMENTS"). Unless otherwise
defined herein, capitalized terms have the meanings set forth in the Certificate
of Designations.

         This letter agreement shall confirm our agreement to certain
restrictions concerning the conversion of shares of the Company's Series A
Preferred Stock by RAM Trading, Ltd. ("BUYER") as set forth below.

         For good and valuable consideration, the receipt and sufficiency of
which are hereby acknowledged, the Company and Buyer agree and confirm the
following matters:

         Notwithstanding anything in the Transaction Documents to the contrary,
         in no event shall the Company effect any conversion of, and no Buyer
         shall have the right to convert any shares of Series A Preferred Stock
         (the "PREFERRED SHARES") into shares of Common to the extent that,
         after giving effect to such conversion such Buyer (together with such
         Buyer's affiliates), through the conversion of Preferred Shares or
         otherwise, would beneficially own in excess of 9.99% of the number of
         shares of Common outstanding immediately after giving effect to such
         conversion. For purposes of the foregoing sentence, the number of
         shares of Common beneficially owned by Buyer and its affiliates shall
         include the number of shares of Common issuable upon conversion of the
         Preferred Shares with respect to which the determination of such
         sentence is being made, but shall

<Page>

         exclude the number of shares of Common which would be issuable upon (i)
         conversion of the remaining unconverted Preferred Shares beneficially
         owned by Buyer and its affiliates and (ii) conversion or exercise of
         the unconverted or unexercised portion of any other securities of the
         Company beneficially owned by Buyer and its affiliates subject to a
         limitation on conversion analogous to the limitation contained in this
         paragraph. Except as set forth in the preceding sentence, for purposes
         of this paragraph beneficial ownership shall be calculated in
         accordance with Section 13(d) of the Securities Exchange Act of 1934,
         as amended. For purposes of this paragraph, in determining the number
         of outstanding shares of Common, Buyer may rely on the number of
         outstanding shares of Common as reflected in (1) the Company's most
         recent Form 10-Q or Form 10-K, as the case may be, (2) a more recent
         public announcement by the Company or (3) any other notice by the
         Company or its transfer agent setting forth the number of shares of
         Common outstanding. For any reason at any time, upon the written or
         oral request of any Buyer, the Company shall within two (2) Business
         Days confirm orally and in writing to Buyer the number of shares Common
         then outstanding. Each delivery of a notice of election to convert
         shares pursuant to Section 5(a) of the Certificate of Designations will
         constitute a representation by the Buyer that it has evaluated the
         limitation set forth in this paragraph and determined that issuance of
         the full number of shares of Common Stock requested in such conversion
         notice is permitted under this paragraph. In any case, the number of
         outstanding shares of Common shall be determined after giving effect to
         the conversion or exercise of Securities of the Company, including the
         Preferred Shares, by Buyer or its affiliates since the date as of which
         such number of outstanding shares of Common was reported.

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

<Page>

         This letter agreement is effective June 29, 2004 and shall be binding
upon the parties and their respective transferees, successors and assigns.

         If the terms of this letter are acceptable to you, please sign below
where indicated.

                                       Very truly yours,

                                       RAM TRADING, LTD.

                                       By:  Ritchie Capital Management, LLC
                                       Its: Investment Manager

                                       By: /s/ JAMES R. PARK
                                           ------------------------------------
                                           James R. Park
                                           Its: Vice President

Agreed and Accepted this 29th day of June, 2004.

GENAISSANCE PHARMACEUTICALS, INC.

By: /s/ KEVIN RAKIN
   --------------------------------------------
   Name:  Kevin Rakin
   Title: President and Chief Executive Officer

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