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                                                                    Exhibit 10.1

                                 PROMISSORY NOTE

$160,000.00                                                       August 7, 2000
                                                          New Haven, Connecticut

         FOR VALUE RECEIVED, the undersigned, Gualberto Ruano, M.D., Ph.D. (the
"Borrower"), hereby promises to pay to Genaissance Pharmaceuticals, Inc., a
Delaware corporation, or to its order or to such persons as it may designate
from time to time (hereinafter referred to as the "Lender") the principal sum of
ONE HUNDRED SIXTY THOUSAND DOLLARS ($160,000.00) on January 1, 2001 (the
"Maturity Date"). Notwithstanding the foregoing, the principal amount hereof
plus all accrued interest shall be forgiven in its entirety on December 31, 2000
(the "Forgiveness Date") provided that, on such Forgiveness Date, Borrower (i)
is an employee of Lender or a subsidiary of Lender and (ii) has used the
proceeds hereof to pay in full the $160,000 principal amount of the Promissory
Note, dated April 18, 1997, payable by Borrower to Richard E. Kouri.

         INTEREST RATE. This note shall bear interest (computed on the basis of
actual days elapsed and a 365-day year) from the date hereof on the unpaid and
unforgiven principal amount at a rate equal to the lowest applicable federal
rate of interest as set forth in Section 1274 of the Internal Revenue Code of
1986, as amended.

         PREPAYMENT. The Borrower, at its option, shall have the right from time
to time, without premium or penalty, to prepay this note at any time in part or
in whole. The Borrower shall also pay all accrued but unpaid interest at the
time of any such prepayment. Any partial payment of the indebtedness evidenced
by this note shall be applied first to interest hereon accrued to the date of
payment, than to the payment of other amounts (except principal) at the time
unpaid hereunder, and finally to the unpaid principal hereof.

         PAYMENTS. All unforgiven principal and unpaid and accrued interest
shall be paid on the Maturity Date. All payments of principal, interest and
other amounts payable on or in respect of this note or the indebtedness
evidenced hereby shall be made to the Lender at its principal place of business,
which is currently Five Science Park, New Haven, Connecticut 06511, and in
lawful money of the United States of America, in funds immediately available to
the Lender as it may direct. Whenever any payment to be made in respect hereto
becomes due on a day which is a Saturday, Sunday or legal holiday, the maturity
thereof shall be extended to the next succeeding business day and interest
hereon shall accrue at the applicable rate during such extensions.

         EVENTS OF DEFAULT AND ACCELERATION. Each of the following events shall
constitute an event of default (an "Event of Default") hereunder: (a) the
failure to make any payment of principal or interest when due, which failure
continues for 30 days after notice of such failure by the Lender; (b) the
Borrower defaults on any other indebtedness or obligations owed to the Lender;
or (c) the Borrower dies or makes an assignment for the benefit of creditors, or
bankruptcy or similar proceedings are commenced by or against the Borrower, or
all or a substantial part of the Borrower's property is attached or a receiver,
trustee or other custodian is appointed therefor. At the option of the Lender,
this note shall become immediately due and payable without notice or demand upon
the occurrence at any time of any Event of Default, provided, however, that upon
any Event of Default specified in subsection (c) above, this note


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shall become immediately due and payable without any demand, notice or other
action by the Lender.

         COSTS OF COLLECTION. Should the indebtedness evidenced by this note or
any part thereof be collected by action at law, or in bankruptcy, receivership
or other court proceedings, or should counsel be retained for collection of this
note after default, Borrower agrees to pay, upon demand by the Lender, in
addition to principal and interest and other sums, if any, due and payable
hereon, court costs and reasonable attorneys' fees and other collection charges,
together with interest thereon at the rate applicable under this note to amounts
past due, unless prohibited by law, all without relief from valuation or
appraisement laws.

         WAIVER. No delay or omission on the part of the holder in exercising
any right hereunder shall operate as a waiver of such right or of any other
right of such holder, nor shall any delay, omission or waiver on any one
occasion be deemed a bar to or waiver of the same or any other right on any
future occasion. The Borrower and every endorser or guarantor of this note
regardless of the time, order or place of signing waives presentment, demand,
protest and notices of every kind and assents to any one or more extensions or
postponements of the time of payment or any other indulgences, to any
substitutions, exchanges or releases of collateral if at any time there be
available to the holder collateral for this note, and to the additions or
releases of any other parties or persons primarily or secondarily liable.

         DELAWARE LAW; SEAL. All rights and obligations hereunder shall be
governed by the law of the State of Delaware, and this note shall be deemed to
be under seal.


Witness:



/s/ Jean Bernardi                                /s/ Gualberto Ruano
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                                                 GUALBERTO RUANO, M.D., PH.D.

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