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                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                           --------------------------

                                   FORM 10-K/A
                                (Amendment No. 2)

                       FOR ANNUAL AND TRANSITION REPORTS
                    PURSUANT TO SECTIONS 13 OR 15(d) OF THE
                        SECURITIES EXCHANGE ACT OF 1934

(MARK ONE)

<Table>
<C>        <S>
   /X/     ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
           SECURITIES EXCHANGE ACT OF 1934
</Table>

                  FOR THE FISCAL YEAR ENDED: DECEMBER 31, 2002
                                       OR

<Table>
<C>        <S>
   / /     TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
           SECURITIES EXCHANGE ACT OF 1934
</Table>

      FOR THE TRANSITION PERIOD FROM ________________ TO ________________

                         COMMISSION FILE NO. 000-30981

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

                       GENAISSANCE PHARMACEUTICALS, INC.

             (Exact name of registrant as specified in its charter)

<Table>
<S>                                             <C>
                DELAWARE                                     06-1338846
    (State or other jurisdiction of             (I.R.S. Employer Identification No.)
     incorporation or organization)

           FIVE SCIENCE PARK                                   06511
         NEW HAVEN, CONNECTICUT                              (Zip Code)
(Address of principal executive offices)
</Table>

       Registrant's telephone number, including area code: (203) 773-1450

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

Securities registered pursuant to Section 12(b) of the Act:  NONE

Securities registered pursuant to Section 12(g) of the Act:  COMMON STOCK, $.001
PAR VALUE
                                         (Title of each class)

    Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes /X/  No / /

    Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to the
Form 10-K. / /

    Indicate by check mark whether the registrant is an accelerated filer (as
defined in Exchange Act Rule 12b-2). Yes / /  No /X/

    The aggregate market value of voting Common Stock held by non-affiliates of
the registrant (without admitting that any person whose shares are not included
in such calculation is an affiliate) on June 30, 2002 was $26,843,669 based on
the last reported sale price of the Common Stock on the Nasdaq consolidated
transaction reporting system.

    Number of shares of the registrant's class of Common Stock outstanding as of
March 28, 2003: 22,846,897.

                      Documents Incorporated By Reference:

    Items 10, 11, 12, 13 and 15 of Part III (except for information required
with respect to our executive officers which is set forth under "Executive
Officers" in Item 1A of Part I of this report) have been omitted from this
report, since we expect to file with the Securities and Exchange Commission, not
later than 120 days after our fiscal year end, a definitive proxy statement. The
information required by Items 10, 11, 12, 13 and 15 of this report, which will
appear in the definitive proxy statement, is incorporated by reference into
Part III of this report.

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

                                EXPLANATORY NOTE

    The purpose of this Form 10-K/A is to amend and restate in its entirety
Item 7 of our Annual Report on Form 10-K, as amended, for the fiscal year
ended December 31, 2002 entitled "Management's Discussion and Analysis of
Financial Condition and Results of Operations" in response to comments
received by the Securities and Exchange Commission (the "SEC") to our
Registration Statement on Form S-3 as filed with the SEC on November 14,
2003, as amended. This Amendment No. 2 to Form 10-K does not reflect events
occurring after the filing of the original Form 10-K or modify or update
those disclosures affected by subsequent events. No other modifications or
changes have been made to the Form 10-K as originally filed or the exhibits
filed therewith, except for changes to the certifications required by (i)
Rules 13a-14(a)/15d-14(a) promulgated under the Securities Exchange Act of
1934, as amended, and (ii) 18 U.S.C. Section 1350.

                                       2
<Page>

ITEM 7. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND
        RESULTS OF OPERATIONS

    THE FOLLOWING DISCUSSION AND ANALYSIS OF OUR FINANCIAL CONDITION AND THE
RESULTS OF OPERATIONS SHOULD BE READ IN CONJUNCTION WITH THE "SELECTED
FINANCIAL DATA" AND OUR FINANCIAL STATEMENTS AND RELATED NOTES APPEARING
ELSEWHERE IN THIS ANNUAL REPORT ON FORM 10-K.

    THIS ANNUAL REPORT ON FORM 10-K CONTAINS FORWARD-LOOKING STATEMENTS
WITHIN THE MEANING OF SECTION 21E OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED. FOR THIS PURPOSE, STATEMENTS CONTAINED HEREIN THAT ARE NOT
STATEMENTS OF HISTORICAL FACT MAY BE DEEMED TO BE FORWARD-LOOKING STATEMENTS.
 WITHOUT LIMITING THE FOREGOING, THE WORDS "BELIEVES," "ANTICIPATES,"
"PLANS," "EXPECTS" AND SIMILAR EXPRESSIONS ARE INTENDED TO IDENTIFY
FORWARD-LOOKING STATEMENTS. THESE FORWARD-LOOKING STATEMENTS INVOLVE RISKS
AND UNCERTAINTIES AND ARE NOT GUARANTEES OF FUTURE PERFORMANCE. ACTUAL
RESULTS MAY DIFFER MATERIALLY FROM THOSE INDICATED IN SUCH FORWARD-LOOKING
STATEMENTS AS A RESULT OF CERTAIN FACTORS INCLUDING, BUT NOT LIMITED TO,
THOSE SET FORTH UNDER THE HEADING "FACTORS AFFECTING FUTURE OPERATING
RESULTS".

OVERVIEW

    Since our inception, we have incurred significant operating losses, and,
as of December 31, 2002, we had an accumulated deficit of $193.8 million. The
majority of our operating losses have resulted from costs we incurred
developing our HAP-TM- Technology, in our clinical trials and administrative
costs associated with operations. As part of our HAP-TM- Technology platform,
we continue to populate our database with HAP-TM- Marker information for
pharmaceutically relevant genes. As of December 31, 2002 we had a total of
6,188 genes in our database with 1,403 of these genes added during the year
ended December 31 2002 and 3,371 genes added during the year ended December
31, 2001. There is not necessarily any correlation between the costs incurred
in any period and the number of genes added to the database in that period.
This is due to the fact that the size of the gene and, therefore, the amount
of work involved varies from gene to gene. In addition, after a gene is
sequenced it must be analyzed and go through an internal quality assurance
check before it is added to the database. This process may cause a gene
sequenced in one period to be added to the database in a different period.
Furthermore, since additional information about genes continues to be
discovered, we may resequence genes previously included in the database and
do further quality assurance analysis. We expect to dedicate a significant
portion of our resources for the foreseeable future to service our HAP-TM-
Partnership program and STRENGTH program partners, our pharmacogenomics
support services customers, our CARING program and to maintain our HAP-TM-
Technology. To date, our revenue has been primarily from licensing and
service fees from our agreements with AstraZeneca UK Limited, Biogen, Inc.,
Gene Logic, Inc., J&J PRD and Pfizer, Inc., as well as a sublicensing
agreement with Visible Genetics, Inc. and, to a lesser extent, government
grants.

    In August 2002, we announced a restructuring and cost reduction program
to revise our business focus and to better align our operating cost structure
with our current and projected partner needs and projected revenues from our
current and projected partners. The cost reduction program included a
realignment of management responsibilities, a reduction in our workforce, and
a decision to seek partners for all internal product development programs.
The workforce was reduced by 20 percent to 110 employees in the third fiscal
quarter, with the majority of the workforce reductions occurring in the DNA
sequencing facility and related informatics support. We incurred a charge for
severance and related costs of approximately $200,000, which was recorded in
operating results in the third fiscal quarter of 2002. All severance
obligations associated with this workforce reduction had been paid by
December 31, 2002.

    As a result of the restructuring and cost reduction program, we expect
future operating expenses to decrease from prior levels, primarily in
research and development expenses. In addition to reducing


                                       3
<Page>

expenses, our plans and projections reflect a measurable reduction in our
negative operating cash flow. These planned reductions in our negative
operating cash flow assume significant year over year increases in revenues.
There can be no assurance that revenues will continue to increase or that
there will continue to be a decrease in the level of cash used to fund
operations. If we are not successful in increasing revenues or reducing
expenses, as planned, we may not be able to maintain our operations at
planned levels.

    During the second quarter of 2002, we recorded a $6.0 million charge for
the impairment of fixed assets. This charge relates to sequencing equipment,
computer hardware and software and leasehold improvements in our DNA
sequencing facility that we determined needed to be reviewed for potential
impairment. As a result of our review, we determined that the carrying value
of the assets was in excess of discounted future cash flows to be generated
by the asset group and we recorded a write-down of $6.0 million. We continue
to review our fixed assets for potential impairment and, based upon our
current cash flow projections, have determined that there has not been an
additional impairment of our fixed assets.

    In November 2002, we announced that we had amended our agreement with a
customer which accounted for 46% of our revenue for the year ended December
31, 2002. The amendment clarifies the intellectual property rights granted
pursuant to the agreement. This agreement expires in the fourth quarter of
2003 unless an extension is negotiated. An agreement with a customer that
accounted for 25% of our revenue for the year ended December 31, 2002,
expired in the fourth quarter of 2002.

    In December, 2002, we announced that we received a notice from General
Electric Capital Corporation (GE) claiming that an event of default had
occurred under our lease agreement as a result of an alleged material adverse
change in our business. We also received a notice from Finova Capital
Corporation (Finova), stating that as a result of the default claim by GE,
there was a cross-default under our agreement with Finova. Both lessors
declared that all principal and future interest obligations were immediately
due and payable. In March 2003, we settled the claim with GE and
simultaneously amended our lease agreement (GE Amendment). In connection with
the GE Amendment, and as additional security for our payment obligations to
GE, we delivered to GE a $2.0 million irrevocable letter of credit and agreed
to additional covenants. It is expected that the letter of credit will be
adjusted on a quarterly basis commencing October 1, 2003 based on a decrease
in outstanding amounts due to GE, as defined. In connection with the
amendment, GE retroactively rescinded their default claim. The GE Amendment
and letter of credit has been retroactively reflected in the accompanying
2002 financial statements. We have not entered into a settlement agreement
with Finova. Accordingly, we have recorded an additional charge to interest
expense to reflect the remaining interest and principal currently due and
payable under the Finova capital lease agreement.

CRITICAL ACCOUNTING POLICIES AND ESTIMATES

    Our financial statements have been prepared in accordance with accounting
principles generally accepted in the United States of America (GAAP). Our
significant accounting policies are described in Note 1 to the Financial
Statements. The preparation of financial statements in accordance with GAAP
requires management to make estimates and assumptions that affect the amounts
reported in the Financial Statements and accompanying footnotes. We base our
estimates on historical experience and on various other assumptions that we
believe to be reasonable under the circumstances, the results of which form
our basis for making judgments about the carrying values of assets and
liabilities that are not readily apparent from other sources. Actual results
may differ from estimates under different conditions, sometimes materially.
Critical accounting policies and estimates are defined as those that are both
most important to the portrayal of our financial condition and results and
require management's most subjective judgments.


                                       4
<Page>

    Our critical accounting policies are as follows:

    - Revenue recognition

    - Valuation of long-lived assets

    - Research and development expenses

    REVENUE RECOGNITION.  We recognize license and service revenue from our
agreements with third parties. The revenue includes fees we receive for the
license of our HAP-TM- database and proprietary software, milestone payments
based on the achievement of certain goals and services fees for providing
specific data on genetic variation. Upfront, non-refundable fees received in
connection with an agreement are deferred and amortized into revenue over the
term of the agreement. License revenues are recognized ratably over the
access period of the agreement. Revenue derived from the achievement of a
milestone is recognized when the milestone is achieved, provided that the
milestone is substantive and a culmination of the earnings process has
occurred. Service fees are recorded as the services are performed. Revenues
derived from the achievement of milestones or recognition of related work
when performed under the terms of a contract, as well as the access period of
the license agreement, may cause our operating results to vary considerably
from period to period.

    VALUATION OF LONG-LIVED ASSETS. We assess the impairment of long-lived
assets whenever events or changes in circumstances indicate that the carrying
value of the assets may not be recoverable. Factors which could trigger an
impairment review, include:

    - a significant adverse change in the extent or manner in which a
      long-lived asset is being used;

    - a significant adverse change in the business climate that could affect
      the value of a long-lived asset; and

    - a significant decrease in the market value of assets.

    When determining whether the carrying value of the long-lived assets is
recoverable we make certain estimates and assumptions regarding the
undiscounted cash flows and discounted cash flows expected to be generated by
the assets. We determine the discounted future cash flow using a discount
rate determined by our management to be commensurate with the risk inherent
in our current business. A change in our estimates or the manner in which we
use the asset may cause results to vary from period to period.

    RESEARCH AND DEVELOPMENT EXPENSES. We record research and development
expenses when they are incurred or, in the case of clinical trial expenses,
based upon information we receive from third party CROs. Research and
development expenses include the following major types of costs: salaries and
benefits, material and reagent costs, research license fees, clinical trial
expenses, depreciation and amortization of lab equipment and leasehold
improvements and building and utility costs related to research space. Vendor
contractual costs consist primarily of consulting arrangements and certain
clinical trial expenses. We expense clinical trial costs as incurred based on
information we receive from third parties and estimates that we make. Our
estimates may change as additional information becomes available which could
cause results to vary from period to period.


                                       5
<Page>

RESULTS OF OPERATIONS

    YEARS ENDED DECEMBER 31, 2002 AND 2001

    Revenue consists primarily of proceeds received in connection with the
licensing of our HAP-TM- Technology, service revenue and sublicensing of
patents. Revenue increased to $8.1 million in 2002 from $5.3 million in 2001.
The increase in license revenues is attributable to the commercialization of
our HAP-TM- Technology, including agreements entered into with Biogen during
2002, AstraZeneca during 2001 and J&J PRD during 2000. Revenue from Gene
Logic, Inc., J&J PRD and Pfizer, Inc. accounted for 82% and 94% of our total
revenue in fiscal 2002 and 2001, respectively. Revenue from each of these
customers accounted for 10% or more of our total revenue for 2002 and 2001,
respectively. Revenue for fiscal 2002 includes a payment received from J&J
PRD in the fourth quarter for achieving a milestone. We are recognizing the
annual license and subscription fees over the term of the agreements and the
service fees as the services are performed. Future milestone and royalty
payments, when and if received, will be recognized when earned. Revenue also
includes the amortization, over the remaining life of the sublicensed patent,
of upfront payments received in connection with the sublicensing of a patent.

    Research and development expenses consist primarily of payroll and benefits
for research and development personnel, materials and reagent costs, costs
incurred in connection with clinical trials, depreciation and maintenance costs
for equipment used for HAP-TM- Marker discovery and HAP-TM- Typing, and
facility-related costs. We expense our research and development costs as
incurred. Research and development costs decreased to $23.9 million in 2002
from $46.3 million in 2001. Except for clinical trial expenses, substantially
all of our research and development expenditures are incurred in processing and
analyzing gene information added to the HAP database. The following is a
breakdown of research and development expense (in thousands):

<Table>

                                  YEAR ENDED DECEMBER 31, 2002      YEAR ENDED DECEMBER 31, 2001
                                  ----------------------------      ----------------------------
<S>                               <C>                               <C>
Payroll and related expenses                       $8,030                           $10,570
Depreciation and amortization                       7,390                             7,850
Consumables                                         1,790                             7,120
Technology license fees                             3,520                             4,670
Repairs and maintenance                             1,040                             1,100
Stock based compensation                              100                               350
Clinical trial expenses                              (720)                            8,740
Other                                               2,750                             5,900
                                                  -------                           -------
Total                                             $23,900                           $46,300
                                                  =======                           =======

</Table>

    The decrease in research and development expenses in 2002 is primarily
attributable to a decrease of approximately $9 million in expenditures related
to our clinical trials, a decrease of approximately $5 million in material and
reagent costs associated with the discovery of new HAP-TM- Markers, a decrease
of approximately $2 million in payroll and related costs and a decrease of
approximately $1 million in technology license fees. The decrease in clinical
trial expenses is primarily due to our STRENGTH Trials, which were
substantially completed by December 31, 2001. The decrease in material and
reagent costs is primarily due to a reduction in DNA sequencing consistent with
the removal of the majority of our ABI Prism(R) 3700 DNA Analyzers from
production in the quarter ended June 30, 2002. The decrease

                                       6
<Page>

in payroll and related costs is primarily due to our work force reduction in
connection with our restructuring program. We expect to continue to devote
substantial resources to research and development expenses in the near future
as we continue to service our HAP-TM- Partnership program and STRENGTH program
partners, our pharmacogenomic support service customers, our CARING program and
to maintain our HAP-TM- Technology. We expect research and development expenses
to decrease modestly in 2003 as a result of the restructuring program that we
initiated in August 2002.

    General and administrative expenses consist primarily of payroll and
benefits for executive, business development, finance, public affairs and
other administrative personnel, as well as facility related costs and outside
professional fees incurred in connection with corporate development, general
legal and financial matters. General and administrative expenses decreased to
approximately $8.8 million in 2002 from $11.9 million in 2001. The decrease
in general and administrative expenses in 2002 is primarily due to a $2
million decrease in consulting and professional service fees and a general
reduction in expenses as part of our cost reduction program initiated during
2002.

    The $6.0 million impairment of fixed assets charge relates to sequencing
equipment, computer hardware and software and leasehold improvements in our
DNA sequencing facility. During the quarter ended June 30, 2002, our
management determined that certain conditions had arisen during the quarter
that triggered the need for a review of our long-lived assets for potential
impairment. These conditions included, but were not limited to, the overall
business climate in which we operate and a significant change in the manner
in which we were utilizing our DNA sequencing facility and related assets. In
particular, during the quarter ended June 30, 2002, we determined that our
sequencing production capacity significantly exceeded our forecasted demand
for the foreseeable future, which resulted in our decision to remove from
production the majority of our ABI Prism(R) 3700 DNA Analyzers, the primary
assets of the group. Accordingly, we performed an impairment review on our
sequencing long-lived assets. As a result of our review, we determined that
the carrying value of the assets was in excess of the projected undiscounted
cash flows to be generated by the asset group. To determine the amount of the
impairment charge, we compared the carrying value of the applicable fixed
assets to their fair value. We determined the fair value of the fixed assets
by discounting expected future cash flows using a discount rate determined by
our management to be commensurate with the risk inherent in our current
business. As a result of our analysis, we determined that the carrying value
of the assets was in excess of discounted future cash flows to be generated
by the asset group and we recorded a write-down of $6.0 million. The
impairment charge has been allocated to the individual assets on a pro-rata
basis. The revised carrying value of the assets is being depreciated over the
average remaining life of the primary assets of the group.

    Interest income decreased to approximately $1.0 million in 2002 from $3.9
million in 2001. The decrease is the result of higher cash, cash equivalent
and short-term investment balances in 2001 and the much lower interest rates
on investments during 2002.

    Interest expense increased to approximately $3.5 million in 2002 from
$2.6 million in 2001. The increase is primarily due to recording additional
interest expense during the quarter ended December 31, 2002, in connection
with certain events of default. In December 2002, we received a notice from
GE claiming that an event of default had occurred under our lease agreement
as a result of an alleged material adverse change in our business. Because of
the alleged default, GE declared that all principal and future interest
obligations were immediately due and payable. GE also filed a complaint in
the Superior Court of the State of Connecticut, demanding payment of all
amounts due under the lease agreement. We also received a notice from Finova,
stating that as a result of the default claim by GE, there was a
cross-default under our agreement with Finova. Finova declared that all
principal and future interest obligations were immediately due and payable.
In March 2003, we settled the claim with GE and simultaneously amended our
lease agreement (GE Amendment). In connection with the amendment, GE
retroactively rescinded their default claim and both parties have withdrawn
from any legal action. As we have not entered into a


                                       7
<Page>

settlement agreement with Finova, we have recorded an additional charge to
interest expense to reflect the fact that all future interest and principal
is currently due and payable under the Finova capital lease agreement. If, in
the future, we enter into a settlement or amend our agreement with Finova it
may result in the reversal, in the period of amendment or settlement, of the
remaining interest expense recognized in the fourth quarter. The status of
the capital lease obligations is discussed further in "Liquidity and Capital
Resources".

    State income tax expense (benefit) decreased to an expense of $35,000 in
2002 from a benefit of $4.1 million in 2001. The benefit represents a net
tax benefit from the State of Connecticut as a result of legislation which
allowed companies to receive cash refunds from the State at a rate of 65% of
their incremental research and development tax credit, as defined, in
exchange for foregoing the carryforward of the research and development tax
credit. The State of Connecticut rescinded the legislation in 2002.

    YEARS ENDED DECEMBER 31, 2001 AND 2000

    Revenue consists primarily of proceeds received in connection with the
licensing of our HAP-TM- Technology, service revenue and sublicensing of
patents. Revenue increased to $5.3 million in 2001 from $753,000 in 2000. The
increase in license revenues is attributable to the commercialization of our
HAP-TM- Technology, including an agreement entered into with Pfizer during
2001, as well as agreements entered into with J&J PRD and Gene Logic, Inc.
during 2000. Revenue from each of J&J PRD, Gene Logic, Inc. and Pfizer, Inc.
accounted for 10% or more of our total revenue in fiscal 2001. J&J PRD, Gene
Logic, Inc. and Visible Genetics, Inc. each accounted for 10% or more of our
total revenue in 2000. We are recognizing the annual license and subscription
fees over the term of the agreements and the service fees as the services are
performed. Future milestone and royalty payments, when and if received, will
be recognized when earned. Revenue also includes the amortization, over the
remaining life of the sublicensed patent, of upfront payments received in
connection with the sublicensing of a patent.

    Research and development expenses consist primarily of payroll and
benefits for research and development personnel, materials and reagent costs,
costs incurred in connection with clinical trials, depreciation and
maintenance costs for equipment used for HAP-TM- Marker discovery and HAP-TM-
Typing, and facility-related costs. Research and development costs increased
to $46.0 million in 2001 from $25.7 million in 2000. Except for clinical
trial expense, substantially all of our research and development expenditures
are incurred in processing and analyzing gene information added to the HAP
database. The following is a breakdown of research and development expense
(in thousands):

<Table>

                                  YEAR ENDED DECEMBER 31, 2001      YEAR ENDED DECEMBER 31, 2000
                                  ----------------------------      ----------------------------
<S>                               <C>                               <C>

Payroll and related expenses                      $10,570                           $ 7,740
Depreciation and amortization                       7,850                             3,290
Consumables                                         7,120                             8,250
Technology license fees                             4,670                             2,410
Repairs and maintenance                             1,100                               160
Stock based compensation                              350                             1,690
Clinical trial expenses                             8,740                               850
Other                                               5,900                             3,010
                                                  -------                           -------
Total                                             $46,300                           $27,400
                                                  =======                           =======
</Table>


                                       8
<Page>

Research and development expenses include stock based and other non-cash
compensation charges for options granted to employees, scientific advisory
board members and consultants. The overall increase in research and
development expenses in 2001 is primarily attributable to an increase in
expenditures related to our clinical trials, the expansion of our HAP-TM-
Typing process, and the increase in resources dedicated to supporting and
improving our proprietary DECOGEN(R) Informatics System. The increase in
expenses includes a $7.9 million increase in costs related to our clinical
trials, a $2.7 million increase in payroll and related costs, a $2.3 million
increase in technology licenses and a $4.6 million increase in depreciation
expense. The decrease in stock based compensation is primarily due to our
decision to vest fully all unvested options previously granted to scientific
advisory board members in March 2000, which resulted in a one-time expense of
approximately $1.4 million.

    General and administrative expenses consist primarily of salary and
related costs for executive, business development, finance, public affairs
and other administrative personnel, as well as facility related costs and
outside professional fees incurred in connection with corporate development,
general legal and financial matters. General and administrative expenses
increased to approximately $11.8 million in 2001 from $8.8 million in 2000.
General and administrative expenses include stock based and other non-cash
compensation charges of $147,000 and $3.6 million for 2001 and 2000,
respectively for options granted to employees, directors and consultants. The
increase in general and administrative expenses in 2001 is primarily due to
increased salary and related costs as a result of the expansion of our
business development activities and the additional costs of operating as a
public company for a full fiscal year. The increase in general and
administrative expenses is partially offset by a decrease in stock based
compensation due to the recording of approximately $2.9 million of expense
during 2000 which related to a stock purchase agreement between two officers
and a former executive officer which we recognized as compensatory and
accordingly recognized non-cash compensation based on the increase in the
fair value of the stock through the date of our initial public offering.

    Sublicensing royalty expense represents royalty obligations incurred by
us on sublicensing fees that we receive. Sublicensing royalty expense
decreased to $54,000 in 2001 from $530,000 in 2000. This decrease relates
primarily to a nonrefundable cash payment received in 2000 in connection with
an amendment to a patent sublicensing agreement. We elected to recognize this
expense in 2000 as paid.

    Interest income (expense), net decreased to approximately $1.3 million in
2001 from $2.8 million in 2000. The decrease is the result of higher cash,
cash equivalent and short-term investment balances in 2000 as a result of
proceeds received from our sale of Series B and Series C preferred stock in
February and March 2000, respectively, and our initial public offering in
August 2000. The decrease is also the result of an increase in interest
expense as a result of higher capital lease and other debt obligations to
fund the acquisition of equipment and partially fund the expansion of our
facilities.

    State income tax benefit of $4.1 million represents a net tax benefit
from the State of Connecticut as a result of recent legislation which allows
companies to receive cash refunds from the State at a rate of 65% of their
incremental research and development tax credit, as defined, in exchange for
foregoing the carryforward of the research and development tax credit.

                                       9
<Page>

LIQUIDITY AND CAPITAL RESOURCES

    We have financed our operations primarily through the private and public
sale of common and preferred stock, government research grants, payments under
licensing agreements, loans and capital leases. From inception through
December 31, 2002, we have received aggregate gross proceeds of approximately
$163.1 million from issuance of common and preferred stock. In addition, through
December 31, 2002, we have received $4.5 million of government grant funding and
$17.8 million from license and service fees, royalties and research contracts.
We also have received $26.2 million from capital lease financing arrangements
and $8.2 million from other loans. Through December 31, 2002, we have acquired
$41.8 million of property and equipment. These assets were largely financed
through capital lease financing arrangements and other loans.

    We expect to continue to finance our operations in the short-term from cash
we received in 2000 from the sale of our common and preferred stock and revenue
from our HAP-TM- Partnership program

                                       10
<Page>

partners and our pharmacogenomics support services customers. Our business
strategy depends on, among other things, entering into partnership agreements
with pharmaceutical and biotechnology companies. If we are unsuccessful in
marketing our partnership programs and pharmacogenomic support services, we may
not generate sufficient revenues to sustain our operations at planned levels.

    Cash used in operations for the year ended December 31, 2002 was
$18.5 million compared with $40.1 million for the same period in 2001. The cash
used in operations for the year ended December 31, 2002 resulted primarily from
a net loss of $33.1 million and a $4.9 million decrease in accounts payable and
accrued liabilities, partially offset by $14.2 million of non-cash charges for
depreciation and amortization expense and impairment of fixed assets, a
$2.6 million increase in deferred revenue and a $2.0 million decrease in other
current assets including the receipt, in September 2002, of $1 million from the
State of Connecticut for the sale of research and development tax credits.

    Cash provided by investing activities was $18.8 million in 2002 compared
with $2.5 million in 2001. In 2002, we used cash to purchase $70,000 of property
and equipment and received proceeds of $28.5 million from the liquidation of
investments in marketable securities and used cash to purchase $9.6 million of
marketable securities.

    Cash used in financing activities was $9.0 million in 2002 compared to
$6.4 million in 2001. During 2002, we repaid debt of approximately $6.9 million
and were required to provide cash collateral of $2.1 million in connection with
the letter of credit issued as part of the GE Amendment.

    Our contractual cash obligations as of December 31, 2002, are as follows:

<Table>
<Caption>
                                                             PAYMENTS DUE BY PERIOD
                                                                 (IN THOUSANDS)
                                     -----------------------------------------------------------------------
                                                              FISCAL YEARS    FISCAL YEARS     FISCAL YEAR
CONTRACTUAL OBLIGATIONS               TOTAL     FISCAL 2003   2004 AND 2005   2006 AND 2007   2008 AND LATER
-----------------------              --------   -----------   -------------   -------------   --------------
<S>                                  <C>        <C>           <C>             <C>             <C>
Long-Term Debt, including
  interest.........................  $ 6,472      $   704        $1,408          $1,408           $2,952
Capital Lease Obligations..........   11,187       11,187*           --              --               --
Operating Leases...................    9,230        1,178         2,235           2,025            3,792
Minimum License Obligations........      500           88           206             206               --
                                     -------      -------        ------          ------           ------
Total Contractual Cash
  Obligations......................  $27,389      $13,157        $3,849          $3,639           $6,744
                                     =======      =======        ======          ======           ======
</Table>

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

*   Reflects all lease obligations as being current. However, as a result of the
    March 2003 GE Amendment, we anticipate paying the outstanding GE lease
    obligation under the original maturity schedule through February, 2005.

    Long-term debt consists primarily of three financing agreements with
Connecticut Innovations, Inc. (CII), a stockholder of the Company, used to
finance certain leasehold improvements and other costs associated with our
facility expansion. Each agreement provides for interest only for a certain
period with principal payments, based on a 120 month amortization, beginning in
April 2001 through October 2002, and with final balloon payments due in
March 2009 through June 2011. Borrowings under the agreements bear interest at
6.5% and are secured by the related leasehold improvements. The Company was in
compliance with all debt covenants as of December 31, 2002 and no cross default
provisions exist in the agreements.

    Capital lease obligations, related to equipment, consist principally of
arrangements with four equipment leasing companies. The leases have terms
ranging from two to four years with installments originally scheduled to end
between August 2003 and October 2004 and which bear interest at rates ranging
from 8.15% to 12.46%. The majority of the capital lease arrangements allow for
the purchase of the related equipment at the completion of the lease term, as
defined in the agreements, and certain of the agreements require the purchase of
the equipment at the completion of the lease term. In

                                       11
<Page>

December 2002, the Company announced it received a notice from GE claiming that
an event of default had occurred under the lease agreement as a result of an
alleged material adverse change in the Company's business. Because of the
alleged default, GE declared that all principal and future interest obligations
were due and payable immediately. GE also filed a complaint in the Superior
Court of the State of Connecticut, demanding payment of all amounts due under
the lease agreements. The Company also received a notice from Finova, stating
that as a result of the alleged default claim by GE, there was a cross-default
under the Company's agreement with Finova. In connection with a cross-default,
Finova declared that all principal and future interest obligations were due and
payable immediately. In March 2003, the Company and GE agreed to an amendment to
their existing lease agreement. In connection with this amendment, GE has
rescinded and withdrawn its default claim and both parties have withdrawn from
any legal action. The lease amendment requires certain additional covenants as
well as a $2 million letter of credit, which is collateralized by cash. Because
of the outstanding claim of default by Finova, the Company recorded an
additional charge to interest expense during 2002. This charge represents all
future interest payments due under the terms of the agreement with Finova. As of
December 31, 2002, the Company has classified as current the GE and Finova lease
obligations, as a result of continuing material adverse change provisions within
the GE agreement and as a result of the Finova default claim.

    We lease our operating facilities located in New Haven, Connecticut. The
lease agreements require annual lease payments of $816,000 per year increasing
to $1.1 million per year over the original term which expires in 2006. We have
two five-year renewal options to extend the lease agreements beyond the initial
term. We are recording the expense associated with the lease on a straight-line
basis over the expected term of the lease. In addition to the operating lease
agreements for our current facility, we also have operating leases for various
office equipment.

    In addition, we periodically enter into agreements with third parties to
obtain exclusive or non-exclusive licenses for certain technologies. The terms
of certain of these agreements require us to pay future royalty payments and
certain milestone payments based on product sales or sublicense income generated
from applicable technologies, if any. The amount of such payments will depend
upon successful commercialization of applicable technologies, if any. The future
minimum payments (assuming non-termination of these leases) are included in the
minimum license obligations above.

    Capital expenditures are not expected to exceed $500,000 to $1 million for
each of fiscal 2003 and 2004.

    Our cash requirements will vary depending upon a number of factors, many of
which are beyond our control, including:

    - the demand for our HAP-TM- Technology;

    - the efforts and success of our HAP-TM- Partnership program;

    - the commercialization of intellectual property derived from our
      associations;

    - the level of competition we face;

    - our ability to maintain our HAP-TM- Technology; and

    - our ability to manage effectively our operating expenses.

    On December 31, 2002, cash, cash equivalents and short-term investments
totaled $34.2 million, which includes $2.1 million of restricted cash, compared
to approximately $59.7 million at December 31, 2001. Our cash reserves are held
in interest-bearing, high-grade corporate bonds and money market accounts. We
believe that our existing cash reserves will be sufficient to fund our expected
net losses, debt obligations and capital expenditures for at least 12 months. To
execute our business plan, we will need to grow our revenues significantly each
year and we may need to seek

                                       12
<Page>
additional funding through public or private equity offerings, debt financings
or commercial partners. We cannot assure you that we will obtain additional
partners or capital funding on acceptable terms, if at all.

INCOME TAXES

    We have not generated any taxable income to date and, therefore, have not
paid any federal income taxes since inception. On December 31, 2002, we had
available unused net operating loss carryforwards of approximately
$121.1 million and $120.1 million, which may be available to offset future
federal and state taxable income, respectively. Use of our federal and state net
operating loss carryforwards, which will begin to expire in 2007 and 2003,
respectively, may be subject to limitations. The future utilization of these
carryforwards may be limited due to changes within our current and future
ownership structure as defined within the income tax code. We have recorded a
full valuation allowance against our deferred tax asset, which consists
primarily of net operating loss carryforwards, because of uncertainty regarding
its recoverability, as required by Statement of Financial Accounting Standards
No. 109 ACCOUNTING FOR INCOME TAXES.

RECENT ACCOUNTING PRONOUNCEMENTS

    In June 2002, the Financial Accounting Standards Board (FASB) issued
Statement of Financial Accounting Standards No. 148, ACCOUNTING FOR STOCK-BASED
COMPENSATION--TRANSITION AND DISCLOSURE, AN AMENDMENT OF FASB STATEMENT
NO. 123. SFAS No. 148 amends SFAS No. 123, ACCOUNTING FOR STOCK-BASED
COMPENSATION, to provide alternative methods of transition for a voluntary
change to the fair value-based method of accounting for stock-based employee
compensation. In addition, SFAS No. 148 amends the disclosure requirements of
SFAS No. 123 to require prominent disclosures in both annual and interim
financial statements about the method of accounting for stock-based employee
compensation and the effect of the method used on reported results. SFAS
No. 148 is effective for fiscal years ending after December 15, 2002 for annual
statements and for interim periods ending after December 15, 2002 for interim
financial reports. The Company has adopted the disclosure requirements of SFAS
No. 148 in its financial statements for the year ended December 31, 2002, but
has not determined whether or not it will voluntarily adopt SFAS No. 123 and the
related transition alternatives pursuant to SFAS No. 148.

    In June 2002, the FASB issued Statement of Financial Accounting Standards
No. 146 (SFAS No. 146), ACCOUNTING FOR COSTS ASSOCIATED WITH EXIT OR DISPOSAL
ACTIVITIES (SFAS 146). This Statement addresses financial accounting and
reporting for costs associated with exit or disposal activities and nullifies
Emerging Issues Task Force (EITF) Issue No. 94-3, LIABILITY RECOGNITION FOR
CERTAIN EMPLOYEE TERMINATION BENEFITS AND OTHER COSTS TO EXIT AN ACTIVITY
(INCLUDING CERTAIN COSTS INCURRED IN A RESTRUCTURING). The provisions of SFAS
No. 146 are effective for exit or disposal activities that are initiated after
December 31, 2002, with early application encouraged. We believe the adoption of
this new standard will not have a material impact on either our operating
results or financial position.

    In November 2002 the FASB issued FASB Interpretation No. 45 (FIN 45),
GUARANTOR'S ACCOUNTING AND DISCLOSURE REQUIREMENTS FOR GUARANTEES, INCLUDING
INDIRECT GUARANTEES OF INDEBTEDNESS OF OTHERS (AN INTERPRETATION OF FASB
STATEMENTS NO. 5, 57, AND 107 AND RESCISSION OF FASB INTERPRETATION NO. 34). FIN
45 clarifies the requirements of FASB Statement No. 5 (FAS 5) ACCOUNTING FOR
CONTINGENCIES, relating to a guarantor's accounting for, and disclosure of, the
issuance of certain types of guarantees. FIN 45 requires that upon issuance of a
guarantee, the guarantor must recognize a liability for the fair value of the
obligation it assumes under that guarantee. The initial recognition and
measurement provisions are effective for guarantees issued or modified after
December 31, 2002. The disclosure requirements under FIN 45 are effective for
the Company's fiscal 2002 year-end.

                                       13
<Page>
    In November 2002, the Emerging Issues Task Force (EITF) issued EITF Issue
No. 00-21, REVENUE ARRANGEMENTS WITH MULTIPLE DELIVERABLES. This issue addresses
revenue recognition for arrangements with multiple deliverables which should be
considered as separate units of accounting if the deliverables meet certain
criteria as described in EITF 00-21. This issue is effective for revenue
arrangements entered into in fiscal periods beginning after June 15, 2003. Early
application is permitted.

FACTORS AFFECTING FUTURE OPERATING RESULTS

    THIS ANNUAL REPORT ON FORM 10-K CONTAINS "FORWARD-LOOKING STATEMENTS" WITHIN
THE MEANING OF SECTION 21E OF THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED.
THESE STATEMENTS ARE SUBJECT TO RISKS AND UNCERTAINTIES AND ARE BASED ON THE
BELIEFS AND ASSUMPTIONS OF OUR MANAGEMENT BASED ON INFORMATION CURRENTLY
AVAILABLE TO OUR MANAGEMENT. USE OF WORDS, SUCH AS "BELIEVES," "EXPECTS,"
"ANTICIPATES," "INTENDS," "PLANS," "ESTIMATES," "SHOULD," "LIKELY" OR SIMILAR
EXPRESSIONS, INDICATE A FORWARD-LOOKING STATEMENT. FORWARD-LOOKING STATEMENTS
INVOLVE RISKS, UNCERTAINTIES AND ASSUMPTIONS. CERTAIN OF THE INFORMATION
CONTAINED IN THIS ANNUAL REPORT ON FORM 10-K CONSISTS OF FORWARD-LOOKING
STATEMENTS. IMPORTANT FACTORS THAT COULD CAUSE ACTUAL RESULTS TO DIFFER
MATERIALLY FROM THE FORWARD-LOOKING STATEMENTS INCLUDE THE FOLLOWING:

WE ARE AN EARLY STAGE COMPANY WITH A HISTORY OF LOSSES AND WE EXPECT TO INCUR
NET LOSSES FOR THE FORESEEABLE FUTURE SUCH THAT WE MAY NEVER BE PROFITABLE.

    We have incurred substantial operating losses since our inception. As of
December 31, 2002, we have generated only minimal revenue from our HAP-TM-
Partnership program and our pharmacogenomics support services, and we do not
expect to generate significant revenues for several years, if ever. From
inception through December 31, 2002, we had an accumulated deficit of
approximately $193.6 million. Our losses to date have resulted principally from
costs we incurred in the development of our HAP-TM- Technology, in our clinical
trials and from general and administrative costs associated with operations. We
expect to devote our resources to service our HAP-TM- Partnership program and
STRENGTH program partners, our pharmacogenomics support services customers, our
CARING program and to maintain our HAP-TM- Technology.

    We expect to incur additional losses this year and in future years, and we
may never achieve profitability. In addition, pharmaceutical and biotechnology
companies are only now beginning to use products such as ours in their drug and
diagnostic development or marketing efforts and, accordingly, they may not
choose to use our HAP-TM- Technology. We do not expect our losses to be
substantially mitigated by revenues from our HAP-TM- Partnership and STRENGTH
programs and our CARING program, if any, or from our pharmacogenomics support
services for a number of years, if ever.

WE CURRENTLY RELY ON A LIMITED NUMBER OF LICENSING AND SERVICE ARRANGEMENTS FOR
SUBSTANTIALLY ALL OF OUR REVENUES. AS A RESULT, THE LOSS OF ONE MAJOR CUSTOMER
OR OUR INABILITY TO SECURE ADDITIONAL SIGNIFICANT CUSTOMERS DURING A GIVEN
PERIOD WOULD HAVE AN ADVERSE AFFECT ON OUR BUSINESS AND OPERATING RESULTS.

    We are dependent upon a limited number of licensing and service arrangements
that represent substantially all of our revenues. In the year ended
December 31, 2002, three of our customers accounted for 82% of our total
revenues. The agreement with the first customer expired by its terms in the
fourth quarter of 2002. The agreements with the second and third customers
terminate by their terms in the third quarter of 2004 and the fourth quarter of
2003, respectively. If we are unable to replace, upon substantially similar
terms, the agreement that expired in 2002 or if we lose either of the remaining
significant customers, it would have a material adverse affect on our revenues
and on our business in general and could cause volatility or a decline in our
stock price.

                                       14
<Page>
TO GENERATE SIGNIFICANT REVENUES, WE MUST OBTAIN ADDITIONAL CUSTOMERS FOR OUR
HAP-TM- PARTNERSHIP PROGRAM AND OUR STRENGTH AND CARING PROGRAMS.

    Our strategy depends on entering into agreements with pharmaceutical and
biotechnology companies for our HAP-TM- Partnership program and our STRENGTH and
CARING programs. We currently have a HAP-TM- Partnership program with six
pharmaceutical and biotechnology companies as well as an agreement with a major
diagnostic company to commercialize exclusively the diagnostic rights and
non-exclusively the product development rights from our STRENGTH program. We may
not obtain additional partners for our HAP-TM- Partnership program and our
STRENGTH program or obtain any partners for our CARING program. If we are
unsuccessful in finding additional partners for our HAP-TM- Partnership program
and our STRENGTH program or in finding any partners for our CARING program, we
may never generate sufficient revenues to sustain our operations. In addition,
we expect that some of our future HAP-TM- Partnership program collaborations,
like some of our current HAP-TM- Partnership program collaborations, will be
limited to specific, limited-term projects or that some of these collaborations
may not be renewed. Accordingly, we must continually obtain new customers to be
successful. To date, the integration of pharmacogenomics into drug development
and marketing has not achieved widespread market acceptance.

IF THE ESTIMATES WE MAKE, AND THE ASSUMPTIONS ON WHICH WE RELY, IN PREPARING OUR
FINANCIAL STATEMENTS PROVE INACCURATE, OUR ACTUAL RESULTS MAY VARY FROM THESE
REFLECTED IN OUR PROJECTIONS AND ACCRUALS.

    Our financial statements have been prepared in accordance with accounting
principles generally accepted in the United States of America. The preparation
of these financial statements requires us to make estimates and judgments that
affect the reported amounts of our assets, liabilities, revenues and expenses,
the amounts of charges accrued by us and related disclosure of contingent assets
and liabilities. We base our estimates on historical experience and on various
other assumptions that we believe to be reasonable under the circumstances.
There can be no assurance, however, that our estimates or the assumptions
underlying our estimates will be correct.

WE MAY REQUIRE ADDITIONAL FUNDING TO FUND OPERATIONS AND REPAY DEBT AND WE MAY
NOT BE ABLE TO OBTAIN ANY.

    We have used substantial amounts of cash to fund our research and
development activities. We will continue to spend funds to service our HAP-TM-
Partnership program and SRENGTH program partners, our pharmacogenomics support
services customers, our CARING program and to maintain our HAP-TM- Technology.
We plan to pay for these activities with funds from:

    - our existing cash and investment securities and

    - income that we may receive from our HAP-TM- Partnership program and
      STRENGTH program partners and pharmacogenomics support services customers.

    We intend to rely on our current HAP-TM- Partnership program and STRENGTH
program partners and future partners, if any, and our current pharmacogenomics
support services customers and future customers, if any, for significant funding
in the future to support our development efforts. To execute our business plans,
we will need to grow our revenues significantly each year. We cannot be certain
when we will begin to receive additional income, if at all, from our HAP-TM-
Partnership and STRENGTH programs and our pharmacogenomics support services and
income, if any, from our CARING program. If we do not receive this income or do
not receive it as rapidly as we expect, we would spend our existing cash and
investment securities more rapidly than we currently plan.

    We believe that our existing cash reserves will be sufficient to support our
expected net losses, debt obligations and capital expenditures for at least 12
months. We cannot assure you that we will be able to obtain new partners or to
generate the increased revenues required to meet our business plan

                                       15
<Page>
objectives. In addition, to execute our business plans, we may need to seek
additional funding through public or private equity offerings, debt financings
or commercial partners. We cannot assure you that we will obtain additional
partners or capital funding on acceptable terms, if at all. If we are unable to
generate sufficient revenues or access capital on acceptable terms, we may be
required to (a) obtain funds on unfavorable terms that may require us to
relinquish rights to certain of our technologies or that would significantly
dilute our stockholders and/or (b) significantly scale back current operations.
Either of these two possibilities would have a material adverse effect on our
business.

OUR HAP-TM- TECHNOLOGY MAY NOT ALLOW OUR PARTNERS TO DEVELOP COMMERCIAL PRODUCTS
OR TO INCREASE SALES OF THEIR MARKETED PRODUCTS.

    We developed our HAP-TM- Technology on the assumption that information about
gene variation and gene variation associated with drug response may help drug
development professionals better understand the drug response of particular
populations and complex disease processes. Although the pharmaceutical and
biotechnology industries are increasing their use of genomics in analyzing drug
response and diseases, we are unaware of any successful drug development program
applying population genomics.

    We discover HAP-TM- Markers for pharmaceutically relevant genes. If we are
unable to find HAP-TM- Markers for pharmaceutically relevant genes in a timely
manner, our potential partners may lose confidence in our HAP-TM- Technology and
our company, and this loss in confidence could decrease our ability to generate
revenues. Even if we are able to discover the HAP-TM- Markers for
pharmaceutically relevant genes, this information may not prove to be superior
to genomic variation information discovered by our competitors. Furthermore,
pharmaceutical and biotechnology companies may not choose our HAP-TM- Technology
over competing technologies.

    Our DECOGEN-Registered Trademark- Informatics System may also be less
effective than we expect or may not allow our partners or us to determine a
correlation between drug response and genomic variation. Furthermore, even if
our partners or we are successful in identifying a specific correlation between
drug response and genomic variation based on our HAP-TM- Technology, our
partners may not be able to develop or sell commercially viable products nor may
our partners be able to increase the sales of their marketed products using this
correlation. Accordingly, our HAP-TM- Markers and HAP-TM- Technology may not
improve the development, marketing and prescribing of drugs or the development
and marketing of diagnostics developed by our HAP-TM- Partnership program and
STRENGTH program partners.

IF WE ARE UNABLE TO OBTAIN INTELLECTUAL PROPERTY PROTECTION FOR OUR HAP-TM-
TECHNOLOGY, TRADE SECRETS OR KNOW HOW, WE MAY NOT BE ABLE TO OPERATE OUR
BUSINESS PROFITABLY.

    Our success depends, in part, on our ability to protect our HAP-TM-
Technology, any associations that we find between clinical outcomes and genetic
variation and any other proprietary software, methods and technologies that we
develop, either as a trade secret or under the patent and other intellectual
property laws of the United States and other countries, so that we can prevent
unauthorized entities from using our inventions and proprietary information.
Because patent applications that were filed prior to November 29, 2000 in the
United States are confidential until patents issue, third parties may have filed
patent applications for technology covered by our pending patent applications
without our being aware of those applications, and our patent applications may
not have priority over any patent applications of others. We are aware that
there are other firms or individuals who have discovered, or are currently
discovering, information similar to the information we are discovering, who may
have filed, and in the future are likely to file, patent applications that are
similar or identical to our patent applications.

    Our pending patent applications may not result in issued patents. The patent
positions of pharmaceutical and biotechnology companies, including ours, are
generally uncertain as a result of the

                                       16
<Page>
uncertain state of the patent law in the biotechnology field. There is no
uniform, worldwide policy regarding the subject matter and scope of claims
granted or allowable in biotechnology patents, particularly those involving
genomics. In addition, some interest groups are lobbying for restrictions on
patenting of genetic tests.

IF WE CANNOT ESTABLISH ADDITIONAL COLLABORATIVE RELATIONSHIPS, WE MAY BE UNABLE
TO DEVELOP OR COMMERCIALIZE OUR HAP-TM- TECHNOLOGY AND WE WILL DEPEND ON OUR
PARTNERS TO DEVELOP OR TO CO-DEVELOP PRODUCTS.

    We currently have a HAP-TM- Partnership program with six pharmaceutical and
biotechnology companies as well as an agreement with a major diagnostic company
to commercialize exclusively the diagnostic rights and non-exclusively the
product development rights from our STRENGTH program. We do not currently have
any partners for our CARING program. Under our current strategy, and for the
foreseeable future, we do not expect to develop or market pharmaceutical or
diagnostic products on our own. As a result, our current and future revenues, in
part, will depend on payments from our current HAP-TM- Partnership program and
STRENGTH program partners and our future HAP-TM- Partnership, STRENGTH and
CARING program partners, if any, for either the new products they may develop,
or for increased sales of their existing products, made possible through the use
of our HAP-TM- Technology. If we are unable to attract new HAP-TM- Partnership
program and STRENGTH program partners or any partners for our CARING program, we
may never generate sufficient revenues to sustain our operations.

    Our partners for our HAP-TM- Partnership program and STRENGTH program and
our partners, if any, for our CARING program, will be responsible for
pre-clinical study and clinical development of therapeutic and diagnostic
products and for regulatory approval, manufacturing and marketing of any
products or enhanced marketing claims that result from the application of our
HAP-TM- Technology. Our current agreements and we anticipate that our future
agreements with partners for our HAP-TM- Partnership and STRENGTH programs and
with partners, if any, for our CARING program will allow them significant
discretion in pursuing these activities. We cannot control the amount and timing
of resources that any such current or potential partners will devote to our
programs or potential products. Our HAP-TM- Partnership program and STRENGTH
program arrangements and our CARING program arrangements, if any, may also have
the effect of limiting the areas of research that we may pursue either alone or
with others. Because part of our revenues will be dependent on the successful
commercialization or development of our partners' products, if, for any reason,
a HAP-TM- Partnership program partner or our STRENGTH program partner delays or
abandons its development or commercialization of a product developed using our
HAP-TM- Technology, we may receive reduced royalty or other payments or no
royalty or other payments at all. In addition, because part of our future
revenues will be dependent on the successful commercialization of additional
aspects of our HAP-TM- Partnership and STRENGTH programs with partners and the
successful commercialization of our CARING program with partners, if, for any
reason, a partner delays or abandons its development or commercialization of
these additional aspects of our HAP-TM- Partnership program or STRENGTH program
or its development or commercialization of our CARING program, we may receive
reduced royalty or other payments or no royalty or other payments at all.

    Although we intend to retain the rights to all HAP-TM- Markers, which we
discover as well as to HAP-TM- Markers discovered jointly with our HAP-TM-
Partnership and STRENGTH program partners and with our CARING program partners,
if any, we may not always be able to negotiate the retention of these rights.
Furthermore, disputes may arise in the future over the ownership of rights to
HAP-TM- Markers as well as any other technology we develop with our HAP-TM-
Partnership and STRENGTH program partners or with our CARING program partners,
if any. These and other possible disagreements between our HAP-TM- Partnership
and STRENGTH program partners and us or between our CARING program partners, if
any, and us could lead to delays in the research, development or

                                       17
<Page>
commercialization of their products. These disagreements could also result in
litigation or require arbitration to resolve. Any of these events could prevent
us from effectively marketing our HAP-TM- Technology.

WE INVEST CONSIDERABLE AMOUNTS OF TIME, EFFORT, AND MONEY TO LICENSE OUR HAP-TM-
TECHNOLOGY; AND IF WE ARE UNABLE TO LICENSE OUR TECHNOLOGY, WE MAY NOT GENERATE
SUFFICIENT REVENUE TO SUSTAIN OUR OPERATIONS.

    Our ability to obtain partners for our HAP-TM- Partnership, STRENGTH and
CARING programs will depend in significant part upon the pharmaceutical and
biotechnology industries' acceptance that our HAP-TM- Technology can help
accelerate or improve their drug and diagnostic development and marketing
efforts. To achieve market acceptance, we must continue to educate the
pharmaceutical and biotechnology industries and the public in general as to the
potential benefits of our HAP-TM- Partnership, STRENGTH and CARING programs.
Most importantly, we must convince the research and development, clinical and
marketing departments of pharmaceutical and biotechnology companies that our
HAP-TM- Technology can accelerate and improve the processes for developing,
marketing and prescribing drugs and for developing and marketing diagnostics and
that our HAP-TM- Partnership, STRENGTH and CARING programs will be commercially
viable. If we fail to gain this acceptance, we may never generate sufficient
revenues to sustain our operations. We may expend substantial funds and
management effort to market our HAP-TM- Partnership, STRENGTH and CARING
programs, without any resulting revenues.

OUR ABILITY TO MAKE ANY ACQUISITIONS IS DEPENDENT ON THE AVAILABILITY OF
ADEQUATE CASH AND THE ATTRACTIVENESS OF OUR STOCK PRICE.

    We anticipate that any future acquisitions of businesses or technologies
will be financed through cash from operations, the issuance of shares of our
common stock and/or seller financing. We cannot assure you that we will have
sufficient existing capital resources or that we will be able to raise
sufficient additional capital resources on terms satisfactory to us, if at all,
in order to meet our capital requirements for such acquisitions.

    We also believe that a significant factor in our ability to close
acquisitions will be the attractiveness of our common stock for potential
acquisition candidates. This attractiveness may, in large part, be dependent
upon the relative market price and capital appreciation prospects of our common
stock compared to the equity securities of our competitors. The trading price of
our common stock on the Nasdaq National Market has affected and, could in the
future materially adversely affect, our acquisition program.

INTEGRATION OF ACQUISITIONS OR STRATEGIC INVESTMENTS COULD INTERRUPT OUR
BUSINESS AND OUR FINANCIAL CONDITION COULD BE HARMED.

    From time to time, we may acquire or make strategic investments in other
businesses or technologies. Any acquisitions or strategic investments we may
make in the future may entail numerous risks that include the following:

    - difficulties integrating acquired operations, personnel, technologies or
      products, if any;

    - diversion of management's focus from our core business concerns;

    - entering markets in which we have no or limited prior experience or
      knowledge;

    - exposure to litigation from stockholders or creditors of, or other parties
      affiliated with, the target company or companies;

    - dilution to existing stockholders and earnings per share; and

    - incurrence of substantial debt.

                                       18
<Page>
    Any such difficulties encountered as a result of any mergers, acquisitions
or strategic investments could adversely affect our business, operating results
and financial condition.

IF WE ARE UNABLE TO PREVENT OTHERS FROM UNAUTHORIZED USE OF, OR ARE UNABLE TO
DEFEND OUR USE OF, OUR HAP-TM- TECHNOLOGY, TRADE SECRETS OR KNOW HOW, WE MAY NOT
BE ABLE TO OPERATE OUR BUSINESS PROFITABLY.

    Despite our efforts to protect our proprietary rights, unauthorized parties
may be able to obtain and use information that we regard as proprietary. The
mere issuance of a patent does not guarantee that it is valid or enforceable;
thus, even if we obtain patents, they may not be valid or enforceable against
third parties.

    We also rely upon unpatented trade secrets and improvements, unpatented
know-how and continuing technological innovation to develop and maintain our
competitive position. We generally protect this information with reasonable
security measures, including confidentiality agreements signed by our employees,
academic collaborators and consultants that provide that all confidential
information developed or made known to others during the course of the
employment, consulting or business relationship will be kept confidential except
in specified circumstances. Agreements with employees, consultants and
collaborators generally provide that all inventions conceived by the individual
while employed by us are our exclusive property. If employees, consultants or
collaborators do not honor these agreements, we may not have adequate remedies
for breach. Furthermore, our trade secrets may otherwise become known or be
independently discovered by competitors.

    Further, a patent does not provide the patent holder with freedom to operate
in a way that infringes the patent rights of others. A third party may sue us
for infringing on its patent rights. Likewise, we may need to resort to
litigation to enforce a patent issued to us or to determine the scope and
validity of third party proprietary rights. The cost to us of any litigation or
other proceeding relating to intellectual property rights, even if resolved in
our favor, could be substantial, and the litigation would divert our
management's efforts. Some of our competitors may be able to sustain the costs
of complex patent litigation more effectively than we can because they have
substantially greater resources. Uncertainties resulting from the initiation and
continuation of any litigation could limit our ability to continue our
operations.

    If any party should successfully claim that the creation or use of our
HAP-TM- Technology or HAP-TM- Marker association data infringe upon their
intellectual property rights, in addition to any damages we might have to pay, a
court could require us to stop the infringing activity or obtain a license on
unfavorable terms. Moreover, any legal action against us or our HAP-TM-
Partnership and STRENGTH program partners or any CARING program partners
claiming damages or seeking to enjoin commercial activities relating to the
affected products and processes could, in addition to subjecting us to potential
liability for damages, require us or our HAP-TM- Partnership and STRENGTH
program partners or any CARING program partners to obtain a license in order to
continue to manufacture or market the affected products and processes. Any
license required under any patent may not be made available on commercially
acceptable terms, if at all. In addition, some licenses may be non-exclusive,
and, therefore, our competitors may have access to the same technology licensed
to us. If we fail to obtain a required license or are unable to design around a
patent, we may be unable to market effectively some of our HAP-TM- Technology,
which could limit our profitability and possibly prevent us from generating
revenue sufficient to sustain our operations.

REGULATORY OVERSIGHT OF OUR HAP-TM- TECHNOLOGY AND PUBLIC OPINION REGARDING
ETHICAL ISSUES SURROUNDING THE USE OF GENETIC INFORMATION MAY ADVERSELY AFFECT
OUR ABILITY TO MARKET OUR HAP-TM- TECHNOLOGY.

    Currently, there is limited FDA regulation of genetic tests. The Secretary's
Advisory Committee on Genetic Testing, an advisory panel to the Secretary of the
U.S. Department of Health and Human Services, has recommended that the FDA
expand its regulation of genetic testing to require FDA

                                       19
<Page>
approval for all new genetic tests and labeling of genetic tests. If the FDA
adopts this recommendation, it may require that we, or our partners, apply for
FDA approval as a prerequisite to marketing genetic tests that incorporate our
HAP-TM- Technology. If the FDA were to deny any application of this kind, it
could adversely affect our business and we may be unable to generate sufficient
revenues to sustain our operations.

    To date, the FDA has not required, in connection with approving any drug,
that a physician must have genomic variation information determined about a
patient before the doctor prescribes a drug. However, the FDA, in one instance,
has required that a physician must have gene expression information about a
patient before the doctor prescribes the drug. On January 31, 2003, the FDA
announced an initiative to help make innovative medical technology available
sooner, including the use of pharmacogenomics during drug development. The FDA
indicated that within six months the agency would issue guidance on when and how
to submit pharmacogenomic information to the FDA during the drug development
process. The FDA said that this guidance would facilitate the exploratory use of
pharmacogenomic screening during drug development and would clarify when such
information would be considered part of the evaluation of drug safety. In
addition, the FDA stated that the agency would hold a workshop in 2003 on issues
that are involved in the co-development of a pharmacogenomic test and a drug and
that within 18 months the agency would issue guidance on the regulatory pathway
for such combinations through the agency's Center for Drug Evaluation and
Research and the Center for Devices and Radiological Health. Our success will
depend in part on what guidance the FDA issues with regard to the use of genomic
variation analysis as part of the drug approval process and, more specifically,
the validity of our HAP-TM- Technology as a basis for identifying genomic
variation and for correlating drug response with genomic variation. Without this
acceptance by the FDA and the pharmaceutical and biotechnology industry, we may
be unable to market effectively our HAP-TM- Technology and we may not generate
sufficient revenues to sustain our operations.

    Within the field of personalized health and medicine, governmental and other
entities may enact patient privacy and healthcare laws and regulations that may
limit the use of genomic variation data. To the extent that these laws and
regulations limit the use of our HAP-TM- Technology or impose additional costs
on our partners, we may be unable to market effectively our HAP-TM- Partnership,
STRENGTH and CARING programs and we may not generate sufficient revenues to
sustain our operations.

    Additionally, public opinion on ethical issues related to the
confidentiality and appropriate use of genetic testing results may influence
governmental authorities to call for limits on, or regulation of the use of,
genetic testing. In addition, governmental authorities or other entities may
call for limits on, or regulation of the use of, genetic testing or prohibit
testing for genetic predisposition to certain conditions, particularly for those
that have no known cure. The occurrence of any of these events could reduce the
potential markets for our HAP-TM- Technology, which could prevent us from
generating sufficient revenues to sustain our operations.

    Furthermore, we may be directly subject to regulations as a provider of
diagnostic information. To the extent that these regulations restrict the sale
of our HAP-TM- Technology or impose other costs, we may be unable to provide our
HAP-TM- Technology to our customers on terms sufficient to recover our expenses.

IF OUR PARTNERS DO NOT SEEK, OR DO NOT RECEIVE, MARKETING APPROVAL FOR PRODUCTS
DEVELOPED, IF ANY, USING OUR HAP-TM- TECHNOLOGY, WE MAY RECEIVE DELAYED ROYALTY
OR OTHER PAYMENTS OR NO ROYALTY OR OTHER PAYMENTS AT ALL.

    Any new drug, biologic, or new drug or biologic indication our partners
develop using our HAP-TM- Technology must undergo an extensive regulatory review
process in the United States and other countries before a new product or
indication of this kind could be marketed. This regulatory process can take many
years and require substantial expense. Changes in FDA policies and the policies
of

                                       20
<Page>
similar foreign regulatory bodies can prolong the regulatory review of each new
drug or biologic license application or prevent approval of the application. We
expect similar delays and risks in the regulatory review process for any
diagnostic product, whenever this regulatory review is required. Even if a
product obtains marketing clearance, a marketed product and its manufacturer are
subject to continuing review. A manufacturer may be forced to withdraw a product
from the market if a previously unknown problem with a product becomes apparent.
Because our future revenues will be largely dependent on the successful
commercialization or development of products using our HAP-TM- Technology, any
delay in obtaining, failing to obtain, or failing to maintain regulatory
approval for a product developed using our HAP-TM- Technology may delay our
receipt of royalty or other payments or prevent us from receiving royalty or
other payments sufficient to recover our expenses.

IF OUR PARTNERS ARE UNABLE TO OBTAIN FDA APPROVAL FOR THERAPEUTIC OR DIAGNOSTIC
PRODUCTS DEVELOPED USING OUR HAP-TM- TECHNOLOGY, THE LACK OF REGULATORY APPROVAL
WILL DIMINISH THE VALUE OF OUR HAP-TM- TECHNOLOGY.

    To date, no one has developed or commercialized any therapeutic product or
commercialized any diagnostic product using our HAP-TM- Technology. We expect to
rely on our partners for our HAP-TM- Partnership and STRENGTH programs and our
partners, if any, for our CARING program to file applications for regulatory
approval and generally direct the regulatory review process and obtain FDA
acceptance of our HAP-TM- Partnership and STRENGTH programs and our CARING
programs, if any. Our partners for our HAP-TM- Partnership and STRENGTH programs
or our partners, if any, for our CARING program, may not submit an application
for regulatory review. Even if they do submit applications, they may not be able
to obtain marketing clearance for any products on a timely basis, if at all. If
our partners fail to obtain required governmental clearances for therapeutic or
diagnostic products, they will not be able to market these products unless and
until they obtain these clearances. As a result, we may not receive royalty or
other payments from our customers. The occurrence of any of these events may
prevent us from generating revenues sufficient to sustain our operations.

IF WE DO NOT SUCCESSFULLY DISTINGUISH AND COMMERCIALIZE OUR HAP-TM- TECHNOLOGY,
WE MAY BE UNABLE TO COMPETE SUCCESSFULLY WITH OUR COMPETITORS OR TO GENERATE
REVENUE SIGNIFICANT TO SUSTAIN OUR OPERATIONS.

    Numerous entities are attempting to identify genomic variation predictive of
specific diseases and drug response and to develop products and services based
on these discoveries. We face competition in these areas from pharmaceutical,
biotechnology and diagnostic companies, academic and research institutions and
government or other publicly-funded agencies, both in the United States and
abroad, most of which have substantially greater capital resources, research and
development staffs, facilities, manufacturing and marketing experience,
distribution channels and human resources than we do.

    These competitors may discover, characterize or develop important
technologies applying population genomics before us or our partners for our
HAP-TM- Partnership and STRENGTH programs that are more effective than those
technologies which we develop or which our partners for our HAP-TM- Partnership
and STRENGTH programs develop, or these competitors may obtain regulatory
approvals of their drugs and diagnostics more rapidly than our partners for our
HAP-TM- Partnership and STRENGTH programs do, any of which could limit our
ability to market effectively our HAP-TM- Technology.

    Some companies and governments are marketing or developing a number of
databases and informatics tools to assist participants in the healthcare
industry and academic researchers in the management and analysis of genomic
data. Entities such as Perlegen Sciences, Celera Genomics Group and the
International HapMap Project have developed or plan to develop databases
containing gene sequence, genomic variation or other genomic information and are
marketing or plan to market their data to pharmaceutical and biotechnology
companies or plan to make freely available their databases. In addition,
numerous pharmaceutical and biotechnology companies, such as GlaxoSmithKline
plc,

                                       21
<Page>
either alone or in partnership with our competitors, are developing genomic
research programs that involve the use of information that can be found in these
databases.

    In order to compete against existing and future technologies, we will need
to demonstrate to potential HAP-TM- Partnership, STRENGTH and CARING program
partners the value of our HAP-TM- Technology and that our HAP-TM- Technology and
capabilities are superior to competing technologies. Although we believe that
our focus on gene-based HAP-TM- Markers, rather than random genomic SNPs or
genome-wide haplotypes, differentiates our HAP-TM- Technology from other
technologies that our competitors are developing, any HAP-TM- Technology
improvements we create may fail to achieve greater market acceptance than the
technologies developed by our competitors.

    Genomic technologies have undergone, and are expected to continue to
undergo, rapid and significant change. Our future success will depend in large
part on maintaining a competitive position in the genomics field. Others may
rapidly develop new technologies that may result in our products or technologies
becoming obsolete before we recover the expenses that we incur in connection
with the development of these products. Our HAP-TM- Technology could become
obsolete if our competitors offer less expensive or more effective drug
discovery and development technologies, including technologies that may be
unrelated to genomics.

IF WE FAIL TO MAINTAIN OUR COMPUTER HARDWARE, SOFTWARE AND RELATED
INFRASTRUCTURE, WE COULD EXPERIENCE LOSS OF, OR DELAY IN, REVENUES AND MARKET
ACCEPTANCE.

    Because our business requires manipulating and analyzing large amounts of
data, we depend on the continuous, effective, reliable and secure operation of
our computer hardware, software and related infrastructure. To the extent that
our hardware or software malfunctions, we will experience reduced productivity.
We protect our computer hardware through physical and software safeguards.
However, our computer hardware is still vulnerable to fire, weather, earthquake,
or other natural disaster and power loss, telecommunications failures, physical
or software break-ins and similar events. In addition, the software and
algorithmic components of our DECOGEN-Registered Trademark- Informatics System
are complex and sophisticated, and as such, could contain data, design or
software errors that could be difficult to detect and correct. Users of our
system may find software defects in current or future products. If we fail to
maintain the necessary computer capacity and data to support our computational
needs and our customers' drug and diagnostic discovery and development efforts,
we could experience a loss in revenues, or a delay in receiving revenues and a
delay in obtaining market acceptance for our technology.

OUR OPERATING RESULTS MAY FLUCTUATE SIGNIFICANTLY AND ANY FAILURE TO MEET
FINANCIAL EXPECTATIONS MAY DISAPPOINT SECURITIES ANALYSTS OR INVESTORS AND
RESULT IN A DECLINE IN OUR COMMON STOCK PRICE.

    Our operating results have fluctuated in the past and we expect they will
fluctuate in the future. These fluctuations could cause our common stock price
to decline. Some of the factors that could cause our operating results to
fluctuate include:

    - recognition of non-recurring revenues due to receipt of license fees,
      achievement of milestones, completion of contracts or other revenues;

    - demand for and market acceptance of our HAP-TM- Partnership, STRENGTH and
      CARING programs;

    - timing of the execution of agreements on our HAP-TM- Partnership, STRENGTH
      and CARING programs and other material contracts;

    - our competitors' announcements or introduction of new products, services
      or technological innovations;

                                       22
<Page>
    - disputes regarding patents or other intellectual property rights;

    - securities class actions or other litigation;

    - adverse changes in the level of economic activity in the United States and
      other major regions in which we do business; and

    - general and industry-specific economic conditions, which may affect our
      partners' use of our HAP-TM- Technology.

    Due to volatile and unpredictable revenues and operating expenses, we
believe that period-to-period comparisons of our results of operations may not
be a good indication of our future performance. It is possible that, in some
future periods, our operating results may be below the expectations of
securities analysts or investors. In this event, the market price of our common
stock could fluctuate significantly or decline.


                                       23
<Page>

                                    PART IV

ITEM 16. EXHIBITS, FINANCIAL STATEMENT SCHEDULE AND REPORTS ON FORM 8-K

(a) 1. FINANCIAL STATEMENTS

       The financial statements are listed under Item 8 of this report.

    2.  FINANCIAL STATEMENT SCHEDULES

    The financial statement schedules listed under Item 8 of this report are
omitted because they are not applicable or required information and are shown in
the financial statements or the footnotes thereto.

(b) REPORTS ON FORM 8-K

    No reports on Form 8-K were filed during the fourth quarter of 2002.

                                       24
<Page>
(c) EXHIBITS

                                 EXHIBIT INDEX

<Table>
<Caption>
EXHIBIT
NUMBER                                    DESCRIPTION OF DOCUMENT
-------                 ------------------------------------------------------------
<C>                     <S>
               3.1(1)   Amended and Restated Certificate of Incorporation.
               3.3(2)   Amended and Restated By-Laws.
               4.1(3)   Form of Common Stock Certificate.
               4.2(3)   Form of Common Stock Purchase Warrant, together with a list
                        of warrant holders.
             10.1*(8)   2000 Amended and Restated Equity Incentive Plan as amended.
            10.1A*(3)   Stock Option Plan.
             10.2*(3)   Employee Stock Purchase Plan 2000.
              10.3(3)   Form of Indemnification Agreement between Genaissance and
                        its directors.
              10.4(3)   Lease Agreement between Genaissance and Science Park
                        Development Corporation dated September 15, 1998.
              10.5(3)   Amendment No. 1 to Lease Agreement between Genaissance and
                        Science Park Development Corporation dated December 1, 1999.
              10.6(3)   Amendment No. 2 to Lease Agreement between Genaissance and
                        Science Park Development Corporation dated December 16,
                        1999.
             10.7*(3)   Genaissance 401(k) Plan
             10.8(3)+   Collaboration Agreement between Genaissance and Telik, Inc.
                        dated February 11, 1998.
              10.9(3)   First Amendment, dated February 11, 1999, to the
                        Collaboration Agreement between Genaissance and Telik, Inc.
                        dated February 11, 1998.
            10.10(3)+   License Agreement between Genaissance and Visible Genetics,
                        Inc. dated November 21, 1996.
            10.11(3)+   Patent License Amending Agreement between Genaissance and
                        Visible Genetics, Inc. dated March 16, 2000.
             10.12(3)   Loan Agreement between Genaissance and Connecticut
                        Innovations, Incorporated dated September 15, 1998.
             10.13(3)   Loan Agreement between Genaissance and Connecticut
                        Innovations, Incorporated dated December 1, 1999.
             10.14(3)   Master Lease Agreement between Genaissance and Finova
                        Technology Finance dated October 2, 1998, and attached
                        Schedules.
             10.15(3)   Letter Agreement with Finova Capital Corporation dated
                        January 24, 2000.
             10.16(3)   Master Equipment Lease Agreement between Genaissance and
                        Oxford Venture Finance dated June 10, 1999, and attached
                        Schedules.
             10.17(3)   Master Lease Agreement between Genaissance and Newcourt
                        Financial USA Inc. dated March 26, 1999, and attached
                        Schedules.
            10.18*(3)   Employment Agreement with Gualberto Ruano dated August 24,
                        1998.
            10.19*(3)   Employment Agreement with Kevin Rakin dated August 24, 1998.
            10.20*(3)   Employment Agreement with Gerald F. Vovis dated April 15,
                        1999.
            10.21*(3)   Confidentiality and Non-Competition Agreement with Richard
                        Judson dated November 16, 1999.
            10.22(3)+   Strategic Alliance Agreement between Genaissance and
                        Sequenom, Inc. dated as of May 3, 2000.
             10.23(3)   Letter Agreement with Finova Capital Corporation dated June
                        7, 2000.
             10.24(3)   Letter Agreement with Connecticut Innovations, Incorporated
                        dated June 2, 2000.
            10.25(3)+   Collaboration Agreement with Gene Logic, Inc. dated June 28,
                        2000.
             10.26(3)   Second Amended and Restated Registration Rights Agreement
                        with the purchasers of Series A and Series KBL Non-voting
                        Preferred Stock dated March 10, 2000.
</Table>

                                       25
<Page>

<Table>
<Caption>
EXHIBIT
NUMBER                                    DESCRIPTION OF DOCUMENT
-------                 ------------------------------------------------------------
<C>                     <S>
             10.27(3)   Amended and Restated Registration Rights Agreement with the
                        purchasers of Series B and Series KBH Preferred Stock dated
                        March 10, 2000.
             10.28(3)   Registration Rights Agreement with purchasers of Series C
                        Preferred Stock dated March 10, 2000.
             10.29(3)   Amendment No. 3 to Lease Agreement between Genaissance and
                        Science Park Development Corporation dated June 1, 2000.
             10.30(3)   Purchase Agreement with Connecticut Innovations,
                        Incorporated dated March 10, 1994.
             10.31(3)   Financing Agreement with Connecticut Innovations,
                        Incorporated dated November 16, 1994.
             10.32(3)   Financing Agreement with Connecticut Innovations,
                        Incorporated dated September 10, 1996.
             10.33(3)   Agreement Concerning Conversion of Convertible Note and
                        Connecticut Presence with Connecticut Innovations,
                        Incorporated dated August 24, 1998.
             10.34(3)   Supplemental Agreement to Agreement Concerning Conversion of
                        Convertible Note and Connecticut Presence with Connecticut
                        Innovations, Incorporated dated November 23, 1999.
             10.35(3)   Letter Agreement with Connecticut Innovations, Incorporated
                        dated February 17, 2000.
             10.36(3)   Loan and Security Agreement and Promissory Note with
                        Transamerica Business Credit Corporation dated April 30,
                        1999.
            10.37*(4)   Employment Agreement with Kenneth B. Kashkin dated September
                        13, 2000.
            10.38*(4)   Promissory Note with Gualberto Ruano dated August 7, 2000.
            10.39*(4)   Promissory Note with Kevin Rakin dated August 7, 2000.
            10.40(5)+   Collaboration Agreement with Janssen Research Foundation
                        dated November 22, 2000.
             10.41(5)   Third Loan Agreement with Connecticut Innovations,
                        Incorporated dated July 26, 2000.
            10.42(6)+   Agreement with Pfizer Inc. dated August 29, 2001.
            10.43(6)+   HAP-TM- Focus Trial License Agreement with AstraZeneca UK
                        Limited dated as of November 29, 2001.
            10.44(6)+   Mednostics-TM- Collaboration and License Agreement with
                        Biogen, Inc. dated as of January 31, 2002.
            10.45(6)+   International Sales Representative Agreement with Intec Web
                        and Genome Informatics Corporation dated as of February 4,
                        2002.
            10.46(6)+   Amendment, dated December 27, 2001, to Collaboration
                        Agreement with Gene Logic, Inc. dated June 28, 2000.
            10.47(6)+   HAP-TM- Focus Trial License Agreement with Biogen, Inc.
                        dated December 21, 2001.
             10.48(6)   Form of Registration Rights Agreement Waiver dated February
                        18, 2002.
            10.49*(6)   Employment Agreement with Richard Judson dated November 20,
                        2001.
             10.50(6)   Fourth Amendment to Lease between Science Park Development
                        Corporation and Genaissance dated September 30, 2001.
             10.51(6)   Amendment, dated May 13, 2002, to Agreement with Pfizer Inc.
                        dated August 29, 2001.
            10.52*(7)   First Amendment, dated September 1, 2002, to Employment
                        Agreement with Gualberto Ruano dated August 24, 1998.
            10.53*(7)   First Amendment, dated September 1, 2002, to Employment
                        Agreement with Kevin Rakin dated August 24, 1998.
            10.54+(7)   Amendment, dated November 22, 2002, to Collaboration
                        Agreement with Janssen Research Foundation dated November
                        22, 2000.
            10.55+(7)   Amendment, dated December 18, 2002, to Mednostics-TM-
                        Collaboration and License Agreement with Biogen, Inc. dated
                        as of January 31, 2002.
            10.56+(7)   Agreement with Pharmacia & Upjohn Company dated December 12,
                        2002.
</Table>

                                       26
<Page>

<Table>
<Caption>
EXHIBIT
NUMBER                                    DESCRIPTION OF DOCUMENT
-------                 ------------------------------------------------------------
<C>                     <S>
            10.57+(7)   Training and License Agreement with Becton, Dickinson and
                        Company dated December 18, 2002.
              16.1(8)   Letter from Arthur Andersen LLP to the Securities and
                        Exchange Commission, dated June 5, 2002.
                 23.1   Consent of PricewaterhouseCoopers LLP. Filed herewith.
                 31.1   Certification pursuant to Rules 13a-14(a)/15d-14(a)
                        promulgated under the Securities Exchange Act of 1934,
                        as amended. Filed herewith.
                 31.2   Certification pursuant to Rules 13a-14(a)/15d-14(a)
                        promulgated under the Securities Exchange Act of 1934,
                        as amended. Filed herewith.
                 32.1   Statement pursuant to 18 U.S.C. Section 1350. Filed
                        herewith.
                 32.2   Statement pursuant to 18 U.S.C. Section 1350. Filed
                        herewith.
</Table>

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

*   Indicates a management contract or compensatory plan.

+  Confidential treatment requested as to certain portions, which portions have
    been filed separately with the Commission.

(1) Filed as Exhibit 3.2 to Genaissance's Registration Statement on Form S-1
    (File No. 333-35314) and incorporated herein by reference.

(2) Filed as Exhibit 3.4 to Genaissance's Registration Statement on Form S-1
    (File No. 333-35314) and incorporated herein by reference.

(3) Filed as an exhibit with the same number to Genaissance's Registration
    Statement on Form S-1 (File No. 333-35314) and incorporated herein by
    reference.

(4) Filed as an exhibit to Genaissance's Quarterly Report on Form 10-Q (File
    No. 000-30981) for the quarter ended September 30, 2000 and incorporated
    herein by reference.

(5) Filed as an exhibit to Genaissance's Annual Report on Form 10-K (File
    No. 000-30981) for the year ended December 31, 2000 and incorporated herein
    by reference.

(6) Filed as an exhibit to Genaissance's Annual Report on Form 10-K (File
    No. 000-30981) for the year ended December 31, 2001 and incorporated herein
    by reference.

(7) Filed as an exhibit to Genaissance's Annual Report on Form 10-K (File
    No. 000-30981), as amended, for the year ended December 31, 2002 and
    incorporated herein by reference.

(8) Filed as an exhibit to Genaissance's Current Report on Form 8-K (File
    No. 000-30981) filed with the SEC on June 4, 2002 and incorporated herein by
    reference.

(9) Filed as an exhibit to Genaissance's Quarterly Report on Form 10-Q (File No.
    000-30981) for the quarter ended June 30, 2002 and incorporated herein by
    reference.

                                       27
<Page>
                                   SIGNATURES

    Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, as amended, the Registrant has duly caused this
Amendment No. 2 to its Annual Report on Form 10-K to be signed on its behalf
by the undersigned, thereunto duly authorized, in the Town of New Haven,
Connecticut, on February 11, 2004.

<Table>
<S>                                                    <C>  <C>
                                                       GENAISSANCE PHARMACEUTICALS, INC.

                                                       By:               /s/ KEVIN RAKIN
                                                            -----------------------------------------
                                                                           Kevin Rakin
                                                                     CHIEF EXECUTIVE OFFICER
</Table>