<PAGE>   1
================================================================================
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                    FORM 10-Q



(Mark One)


[X]  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
     SECURITIES EXCHANGE ACT OF 1934
     FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 1999.


                                       OR


[ ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
     SECURITIES EXCHANGE ACT OF 1934
     FOR THE TRANSITION PERIOD FROM _______________TO _______________.


                         COMMISSION FILE NUMBER 0-23317

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

                                 GENE LOGIC INC.
             (Exact name of registrant as specified in its charter)

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

          DELAWARE                                     06-1411336
(State or other jurisdiction of                     (I.R.S. Employer
incorporation or organization)                      Identification No.)


                             708 QUINCE ORCHARD ROAD
                          GAITHERSBURG, MARYLAND 20878
                    (Address of principal executive offices)
                                 (301) 987-1700
                (Registrant's phone number, including area code)

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

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 [ ]

The number of shares outstanding of the Registrant's Common Stock, $.01 par
value, was 19,912,425 as of October 31, 1999.

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




<PAGE>   2


                                 GENE LOGIC INC.


                                TABLE OF CONTENTS


<TABLE>
<CAPTION>

PART I         FINANCIAL INFORMATION

Item 1. Financial Statements

<S>                                                                                     <C>
Consolidated Balance Sheets at September 30, 1999 and December 31, 1998..................3
Consolidated Statements of Operations for the Three and Nine Months Ended
                  September 30, 1999 and 1998............................................4
Consolidated Statements of Cash Flows for the Nine Months Ended
                  September 30, 1999 and 1998............................................5
Notes to Consolidated Financial Statements...............................................6

Item 2. Management's Discussion and Analysis
        of Financial Condition and Results of Operations.................................9

Item 3. Quantitative and Qualitative Disclosure About Market Risk ......................15


PART II        OTHER INFORMATION

Item 1. Legal Proceedings...............................................................15

Item 2. Changes in Securities and Use of Proceeds.......................................16

Item 3. Defaults Upon Senior Securities.................................................16

Item 4. Submission of Matters to a Vote of Security Holders.............................16

Item 5. Other Information...............................................................16

Item 6. Exhibits and Reports on Form 8-K................................................16

Signatures .............................................................................17


</TABLE>





                                       2.
<PAGE>   3


PART I         FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

                                 GENE LOGIC INC.
                           CONSOLIDATED BALANCE SHEETS
                      (IN THOUSANDS, EXCEPT PER SHARE DATA)

<TABLE>
<CAPTION>

                                                                                 SEPTEMBER 30,      DECEMBER 31,
                                                                                     1999              1998
                                                                                --------------    --------------
                                                                                 (Unaudited)
                                     ASSETS
<S>                                                                              <C>              <C>
Current Assets:
     Cash and cash equivalents ................................................. $   4,400        $   16,191
     Marketable securities available-for-sale...................................    12,192            14,791
     Due from collaborators.....................................................     3,502             3,779
     Prepaid expenses...........................................................     1,910               842
     Notes receivable from employees............................................        41                 -
     Other current assets.......................................................       825               875
                                                                                 ------------     -------------
                  Total Current Assets..........................................    22,870            36,478
Property and Equipment, net ....................................................    10,796            10,189
Notes Receivable from Employees.................................................       727                 -
Goodwill, net...................................................................     6,104             7,249
Intangible and Other Assets, net ...............................................     2,477             1,650
                                                                                 ------------     -------------
                  Total Assets ................................................. $  42,974        $   55,566
                                                                                 ============     =============

                      LIABILITIES AND STOCKHOLDERS' EQUITY


Current Liabilities:
     Accounts payable .......................................................... $   2,937        $    2,123
     Accrued expenses...........................................................     2,117             2,963
     Accrued restructuring......................................................         -               184
     Current portion of capital lease obligation................................       132               124
     Current portion of long-term debt..........................................     1,307             1,292
     Deferred revenue...........................................................     4,638             3,219
                                                                                 ------------     -------------
                  Total Current Liabilities.....................................    11,131             9,905
Long-Term Debt..................................................................     3,207             3,789
Other Noncurrent Liabilities....................................................       549               584
                                                                                 ------------     -------------
                  Total Liabilities.............................................    14,887            14,278
                                                                                 ------------     -------------
Commitments and Contingencies
Stockholders' Equity:
     Common Stock, $.01 par value; 60,000,000 shares authorized;
      19,905,994 and 19,651,756 shares issued and outstanding as of
      September 30, 1999 and December 31, 1998, respectively....................       199               197
     Preferred Stock, $.01 par value; 10,000,000 shares authorized; no shares
      issued and outstanding as of September 30, 1999 and December 31,
      1998......................................................................         -                 -
     Additional paid-in capital ................................................   103,140           102,670
     Deferred compensation on stock options, net ...............................    (2,934)           (3,986)
     Accumulated other comprehensive loss ......................................       (49)              (46)
     Accumulated deficit .......................................................   (72,269)          (57,547)
                                                                                 ------------     -------------
                  Total Stockholders' Equity....................................    28,087            41,288
                                                                                 ------------     -------------
                  Total Liabilities and Stockholders' Equity.................... $  42,974        $   55,566
                                                                                 ============     =============


</TABLE>


                            See accompanying notes.




                                       3.
<PAGE>   4


                                 GENE LOGIC INC.
                      CONSOLIDATED STATEMENTS OF OPERATIONS
                      (IN THOUSANDS, EXCEPT PER SHARE DATA)
                                   (UNAUDITED)

<TABLE>
<CAPTION>


                                                                      THREE MONTHS ENDED                NINE MONTHS ENDED
                                                                         SEPTEMBER 30,                     SEPTEMBER 30,
                                                                 ----------------------------     ------------------------------
                                                                     1999           1998              1999             1998
                                                                 -----------    -----------       ------------      ----------

<S>                                                              <C>            <C>               <C>               <C>
Revenues........................................................ $    4,223     $    2,743        $    13,502       $   8,618
Expenses:
   Research and development.....................................      7,020          4,090             21,506          11,234
   General and administrative...................................      2,335          1,673              6,094           4,991
   Amortization of goodwill.....................................        381              -              1,143               -
   Acquired in-process research and development.................          -         35,196                  -          35,196
                                                                 -----------    -----------       ------------      ----------
               Total expenses...................................      9,736         40,959             28,743          51,421
                                                                 -----------    -----------       ------------      ----------
               Loss from operations.............................     (5,513)       (38,216)           (15,241)        (42,803)
Interest income, net............................................        126            428                589           1,527
Other income (expense)..........................................          -              -                 30             (80)
                                                                 -----------    -----------       ------------      ----------
               Loss before income tax expense...................     (5,387)       (37,788)           (14,622)        (41,356)
Income tax expense..............................................          -              -                100               -
                                                                 -----------    -----------       ------------      ----------
               Net loss......................................... $   (5,387)    $  (37,788)        $  (14,722)      $ (41,356)
                                                                 ===========    ===========       ============      ==========
Basic and Diluted Net Loss Per Common Share..................... $    (0.27)    $    (2.54)        $    (0.74)      $   (2.88)
                                                                 ===========    ===========       ============      ==========
Shares Used In Computing Basic and Diluted Net Loss
         Per Common Share........................................    19,887         14,906             19,799          14,345
                                                                 ===========    ===========       ============      ==========

</TABLE>

                             See accompanying notes.



                                       4.
<PAGE>   5


                                 GENE LOGIC INC.
                      CONSOLIDATED STATEMENTS OF CASH FLOWS
                                 (IN THOUSANDS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>

                                                                                              NINE MONTHS ENDED
                                                                                               SEPTEMBER 30,
                                                                                    ----------------------------------
                                                                                          1999                1998
                                                                                    --------------      --------------
<S>                                                                                 <C>                 <C>
   Cash Flows From Operating Activities:
   Net loss.......................................................................  $     (14,722)      $     (41,356)
   Adjustments to reconcile net loss to net cash flows from operating
           activities:
           Depreciation and amortization .........................................          2,343               1,141
           Amortization of goodwill...............................................          1,143                   -
           Amortization of deferred compensation .................................          1,148               1,203
           Acquired in-process research and development ..........................              -              35,196
           Loss on disposal of property and equipment.............................              -                  81
   Changes in operating assets and liabilities (net of effects of acquisition):
           Due from collaborators.................................................            277              (1,433)
           Prepaid expenses.......................................................         (1,068)                (69)
           Other current assets...................................................             50                (224)
           Intangibles and other assets...........................................           (937)               (523)
           Accounts payable ......................................................            814                 703
           Accrued expenses.......................................................           (846)                318
           Accrued restructuring .................................................           (184)                  -
           Deferred revenue ......................................................          1,419              (2,815)
           Other noncurrent liabilities...........................................             65                  89
                                                                                    --------------      --------------
                    Net Cash Flows From Operating Activities .....................        (10,498)             (7,689)
                                                                                    --------------      --------------
   Cash Flows From Investing Activities:
           Purchases of property and equipment ...................................         (2,838)             (5,582)
           Increase in notes receivable from employees............................           (768)                  -
           Payment of acquisition costs, net of cash acquired.....................              -                (755)
           Pre-acquisition advances to Oncormed...................................              -              (1,843)
           Proceeds from sale and maturity of marketable securities
               available-for-sale ................................................          2,596                   -
           Purchase of marketable securities available-for-sale...................              -             (10,470)
                                                                                    --------------      --------------
                    Net Cash Flows From Investing Activities......................         (1,010)            (18,650)
                                                                                    --------------      --------------
   Cash Flows From Financing Activities:
           Proceeds from issuance of common stock.................................            376                 340
           Proceeds from equipment loans..........................................              -               4,284
           Proceeds from note payable.............................................            425                   -
           Repayments of financing agreement......................................            (98)               (136)
           Repayments of capital lease obligation,
                 equipment loans and note payable.................................           (986)               (526)
                                                                                    --------------      --------------
                    Net Cash Flows From Financing Activities......................           (283)              3,962
                                                                                    --------------      --------------
   Net Decrease in Cash and Cash Equivalents......................................        (11,791)            (22,377)
   Cash and Cash Equivalents, beginning of period.................................         16,191              46,522
                                                                                    --------------      --------------
   Cash and Cash Equivalents, end of period.......................................  $       4,400       $      24,145
                                                                                    ==============      ==============
   Supplemental Disclosure:
           Interest expense paid..................................................  $         311       $         117
                                                                                    ==============      ==============
   Non-Cash Transactions:
           Issuance of Common Stock in Acquisition ...............................  $           -       $      38,217
                                                                                    ==============      ==============

</TABLE>



                             See accompanying notes.



                                       5.
<PAGE>   6


                                 GENE LOGIC INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                               SEPTEMBER 30, 1999
                                   (UNAUDITED)



NOTE 1.  SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation

     The unaudited consolidated financial statements include the accounts of
Gene Logic Inc. and its wholly owned subsidiary (the "Company"). The
accompanying unaudited consolidated financial statements have been prepared in
accordance with generally accepted accounting principles for interim financial
information and with the instructions to Form 10-Q and Article 10 of Regulation
S-X. The consolidated balance sheet as of September 30, 1999, consolidated
statements of operations for the three and nine months ended September 30, 1999
and 1998 and the consolidated statements of cash flows for the nine months ended
September 30, 1999 and 1998 are unaudited, but include all adjustments
(consisting of normal recurring adjustments) which the Company considers
necessary for a fair presentation of the financial position, operating results
and cash flows for the periods presented. Although the Company believes that the
disclosures in these financial statements are adequate to make the information
presented not misleading, certain information and footnote information normally
included in financial statements prepared in accordance with generally accepted
accounting principles have been condensed or omitted pursuant to the rules and
regulations of the Securities and Exchange Commission.

     Results for any interim period are not necessarily indicative of results
for any future interim period or for the entire year. The accompanying unaudited
consolidated financial statements should be read in conjunction with the
financial statements and notes thereto included in the Company's Annual Report
on Form 10-K for the year ended December 31, 1998.

Comprehensive Loss

     The Company accounts for comprehensive loss as prescribed by Statement of
Financial Accounting Standards No. 130, "Reporting Comprehensive Income".
Comprehensive income is the total net income(loss) plus all changes in equity
during the period except those changes resulting from investment by owners and
distribution to owners. The Company's other comprehensive gain (loss) includes
unrealized holding gains(losses) from marketable securities available-for-sale
for the three and nine months ended September 30, 1999 and 1998 as follows:

<TABLE>
<CAPTION>

                                                              THREE MONTHS ENDED            NINE MONTHS ENDED
                                                                 SEPTEMBER 30,                 SEPTEMBER 30,
                                                         ----------------------------   ---------------------------
                                                             1999             1998          1999              1998
                                                         ------------   -------------   ------------   ------------
                                                                 (in thousands)                (in thousands)
<S>                                                      <C>             <C>            <C>             <C>
Net loss ..............................................  $  (5,387)      $  (37,788)    $ (14,722)      $   (41,356)
Other comprehensive loss, net of tax:
     Unrealized gains(losses) on marketable securities.         51                2            (3)              (10)
     Less - Reclassification adjustment for losses ....          -                -             -                 2
                                                         ------------    -------------  -----------     --------------
         Total other comprehensive gain(loss) .........         51                2            (3)               (8)
                                                         ------------    -------------  -----------     --------------
Comprehensive loss ....................................  $  (5,336)      $  (37,786)    $ (14,725)      $   (41,364)
                                                         ============    =============  ===========     ==============

</TABLE>


                                       6.
<PAGE>   7









Goodwill

     Goodwill, from the acquisition of Oncormed, Inc. ("Oncormed") in September
1998, represents the excess of the purchase price over the fair market value of
the net assets acquired. Goodwill is being amortized over five years at a rate
of approximately $1.5 million per year. Amortization expense was $381,000 and
$1.1 million for the three and nine months ended September 30, 1999,
respectively. Accumulated amortization of goodwill was $1.5 million at September
30, 1999.

Revenue Recognition

     Technology and database access fees are recognized evenly over the term of
the Company's collaboration agreements. Revenues from research and development
support are recognized when they are earned which is ordinarily when the work is
performed or costs are incurred. Milestone payments are recognized as revenue in
accordance with the applicable performance requirements and contractual terms.
Revenues from pharmacogenomic services are recognized upon completion of the
services. Revenues for such amounts are deferred until earned.

     Nonrefundable upfront payments received for the value of transferred
technology or other contractual rights that are not contingent upon future
performance under the terms of the collaboration agreements are recognized as
revenue upon execution of the agreements. Under collaboration agreements in
which the Company creates a research database in exchange for a fixed fee,
revenues from such collaborations are recognized on the percentage-of-completion
method, primarily based on man-months incurred to date compared with total
estimated man-months for development of such database.

Software Development Costs

     In accordance with the provisions of the Financial Accounting Standards
Board Statement No. 86, "Accounting for the Costs of Computer Software to be
Sold, Leased or Otherwise Marketed," the Company has capitalized certain
software development costs incurred in developing certain products once
technological feasibility of the products was demonstrated. The Company recorded
capitalized software costs of $517,000 for the three and nine months ended
September 30, 1999. The Company will begin amortization of such costs when the
products are available for general release to customers, which is expected to
occur in the fourth quarter of 1999.

NOTE 2.  ACCRUED RESTRUCTURING

     In connection with the acquisition of Oncormed, the Company recorded a
restructuring liability of approximately $1.6 million. The objective of the
restructuring plan was to eliminate redundant general and administrative
employees of Oncormed and terminate contracts that the Company deemed to have no
on-going economic value to the Company. The restructuring liability consisted of
$373,000 in costs associated with the involuntary termination of ten Oncormed
employees and approximately $1.2 million in contract termination costs. This
liability was included in the purchase price allocation performed in connection
with the acquisition. The restructuring activities as a result of the
acquisition were substantially completed in the third quarter of 1999.









                                       7.
<PAGE>   8


     The following table details the major components of the restructuring
liability relating to the Oncormed acquisition:

<TABLE>
<CAPTION>

                                                                                           CONTRACT
                                                                                         TERMINATION
                                                                      PERSONNEL             COSTS                TOTAL
                                                                  ---------------  ----------------------   ----------------
                                                                                        (in thousands)
<S>                                                               <C>               <C>                     <C>
       Restructuring liability.................................   $        373      $       1,224           $     1,597
       1998 activity ..........................................           (239)            (1,174)               (1,413)
                                                                  ---------------  ----------------------   ----------------
       Balance at December 31, 1998............................            134                 50                   184
       Activity through September 30, 1999.....................           (134)               (50)                 (184)
                                                                  ---------------  ----------------------   ----------------
       Balance at September 30, 1999...........................   $          -      $           -           $         -
                                                                  ===============  ======================   ================

</TABLE>

NOTE 3.  SEGMENT INFORMATION

     At December 31, 1998, the Company adopted Statement of Financial Accounting
Standards No. 131, "Disclosure about Segments of an Enterprise and Related
Information" that establishes standards for reporting information about
operating segments in annual and interim financial statements and related
disclosures about products, services, geographic areas and major customers. The
Company's operations are treated as one operating segment--genomic information
products, software and research services--as the Company only reports loss
information on an aggregate basis to chief operating decision makers of the
Company.

     The following is a breakdown of revenue by major collaborators exceeding
ten percent (10%) of such revenues and by geographic areas:

<TABLE>
<CAPTION>

                                                   MAJOR COLLABORATORS                GEOGRAPHIC AREA
                                               --------------------------       ---------------------------
                                                 A       B      C     D          JAPAN      EUROPE     US
                                               -----  -----   ----   ----       --------  ---------   -----
<S>                                            <C>    <C>     <C>    <C>        <C>       <C>         <C>
   For the three months ended:
    September 30, 1999.......................    48%    26%     -     13%           48%         13%     26%
    September 30, 1998.......................    34%    18%     36%   11%           34%         47%     18%

   For the nine months ended:
    September 30, 1999........................   41%    24%     11%   13%           41%         24%     24%
    September 30, 1998........................   36%    17%     26%   21%           36%         47%     17%

</TABLE>






                                       8.
<PAGE>   9





ITEM 2. MANAGEMENT'S DISCUSSIONS AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
OF OPERATIONS

     The following Management's Discussion and Analysis of Financial Condition
and Results of Operations contains forward-looking statements, including
statements as to the timing of availability of products under development, the
ability to commercialize products developed under collaborations, the
performance and utility of the Company's products and services, and the adequacy
of capital resources. Such statements reflect management's current views of
future events and are subject to risks and uncertainties that could cause actual
results to differ materially from those projections. These risks and
uncertainties include, but are not limited to, the extent of utilization of
genomic information by the pharmaceutical industry in both research and
development, risks relating to the development of genomic database products and
their use by existing and potential collaborators and customers of the Company,
the Company's ability to manage and maintain multiple, concurrent
collaborations, the Company's reliance on collaborators for development and
commercialization of products, the impact of technological advances and
competition, the Company's ability to enforce its intellectual property rights,
the impact of the intellectual property rights of others, the Company's ability
to obtain additional financing on terms favorable to the Company and the
Company's ability to enter into arrangements with new collaborators and to
maintain new and existing collaborations, the ability of the Company to
implement in a timely manner the programs and actions related to the Year 2000
issue, as well as other risks and uncertainties included in the Company's Annual
Report on Form 10-K for the year ended December 31, 1998 filed with the
Securities and Exchange Commission.

     GeneExpress(TM) and Flow-thru Chip(TM) are trademarks of the Company.
GeneChip(R) is a registered trademark of Affymetrix, Inc. ("Affymetrix").

OVERVIEW

     The Company was incorporated in September 1994 and has devoted
substantially all of its resources to the development of its genomics
technologies, bioinformatics systems and database products for use in
pharmaceutical, diagnostic and agricultural product research and development.
The Company has collaborations with the American Home Products Corp.'s
Wyeth-Ayerst Research unit, Hoechst Schering AgrEvo GmbH, Japan Tobacco Inc.,
Merck & Company Inc., NV Organon, a pharmaceutical unit of Akzo Nobel NV,
Procter & Gamble Pharmaceuticals, Rhone-Poulenc Rorer Inc., Schering-Plough
Corp., SmithKline Beecham PLC and UCB Research Inc., a division of UCB Pharma.

     These agreements provide the Company with various combinations of recurring
technology and database access fees, research funding and fees for
pharmacogenomic services, certain additional payments upon the attainment of
research and product development milestones, royalty payments based on sales of
any products resulting from the collaborations, and nonrefundable upfront
payments. Technology and database access fees are recognized evenly over the
term of the Company's collaboration agreements. Revenues from research and
development support are recognized when they are earned which is ordinarily when
the work is performed or costs are incurred. Revenues from pharmacogenomic
services are recognized upon completion of the services. Milestone payments and
royalties are recognized when they are earned in accordance with the applicable
performance requirements and contractual terms. Revenues for such amounts are
deferred until earned. Nonrefundable upfront payments received for the value of
transferred technology or other contractual rights that are not contingent upon
future performance under the terms of the collaboration agreements are
recognized as revenue upon execution of the agreements. The loss of revenues
from any individual material collaboration agreement, if terminated, could have
a material adverse effect on the Company's business, financial condition and
results of operations.

     In an effort to address the growing needs of research and development in
the pharmaceutical industry, the Company is investing significant resources in
building its GeneExpress(TM) databases. These




                                       9.
<PAGE>   10


databases will contain expression information from a wide variety of tissues
from healthy, diseased and drug-treated patients and from experimental animals.
The initial GeneExpress database will incorporate data obtained from GeneChip(R)
probe arrays under an agreement with Affymetrix. The Company commenced marketing
the GeneExpress databases to pharmaceutical companies and expects to receive
subscription fees from such database users in late 1999.

     Gene Logic's future profitability will depend in part on the successful
establishment of collaborations which include various combinations of genomic
databases, bioinformatics software and genomics technology and the successful
commercialization of its GeneExpress databases. Payments through collaborations
and subscriptions to the GeneExpress databases are expected to be the Company's
primary sources of revenue for the foreseeable future. Significant royalties or
other revenues from commercial sales of products developed from any therapeutic,
diagnostic or agricultural product identified using the Company's technologies
are not expected for several years, if at all. Through September 30, 1999,
royalties or other revenues from commercial sales of products paid to Gene Logic
were immaterial. Revenues under collaborations may be subject to significant
fluctuation in both timing and amount, and, therefore, the Company's results of
operations for any period may not be comparable to the results of operations for
any other period. Furthermore, the generation of significant revenues and
profitability will depend upon the Company's ability to enter into additional
collaborations and successfully commercialize its GeneExpress databases. There
can be no assurance that the Company will enter into additional collaborations
on acceptable terms, if at all, or that current or future collaborations will be
successful, or that the Company will be able to successfully commercialize its
GeneExpress databases.

     The Company has incurred operating losses in each year since its inception.
At September 30, 1999, excluding the $35.2 million non-recurring charge incurred
in connection with the acquisition of Oncormed, the Company had accumulated
operating losses of approximately $37.1 million. The Company's losses have
resulted principally from costs incurred in research and development and from
general and administrative costs associated with the Company's operations, in
addition to the charge incurred in connection with the acquisition of Oncormed.
These costs have exceeded the Company's revenues which, to date, have been
generated principally from collaborations. The Company expects to incur
additional operating losses for the foreseeable future, primarily as a result of
increases in its expenses for research and development.

     The Company's quarterly operating results may fluctuate significantly as a
result of a variety of factors, including changes in the demand for the
Company's technologies and products, variations in revenues under
collaborations, including milestone payments, royalties, license fees and other
contract revenues, and the timing of new product introductions, if any, by the
Company. The Company's quarterly operating results may also fluctuate
significantly depending on changes in the research and development budgets of
the Company's collaborative partners, the introduction of new products by the
Company's competitors and other competitive factors, the adoption of new
technologies, and the cost, quality and availability of cell and tissue samples
and related reagents.

UPDATE ON IN-PROCESS RESEARCH AND DEVELOPMENT

     In connection with the acquisition of Oncormed in September 1998, the
Company allocated $35.2 million of the $39.2 million purchase price to
in-process research and development projects. This allocation represents the
estimated fair value based on discounted cash flows related to the incomplete
research and development projects. At the time of acquisition, the progress of
these projects had not yet reached technological feasibility and the projects
had no alternative future uses. Accordingly, these costs were expensed as of the
acquisition date. The in-process research and development value consists of four
technology projects that involve the development of technologies for either
genomic databases or pharmacogenomics.






                                       10.
<PAGE>   11

     At September 30, 1999, additional progress had been achieved on each of the
four technology projects that were underway as of the acquisition. In general,
the Company believes these research and development projects are on track with
management's plans at the time the acquisition occurred. Through September 30,
1999, no significant adjustments have been made in the economic assumptions or
expectations that underlie the Company's acquisition decision and related
purchase accounting. All four in-process research and development projects are
active, and the Company is advancing the technology at a rate consistent with
originally projected completion dates. Specifically, the SNP Analysis Project,
Recognizer Project and Gene Chip / Gene Expression Database Development Project
are substantially complete and the Biorepository Project is expected to be
substantially complete by the end of 1999. Because these technologies are
interrelated with respect to the development of genomic database and
pharmacogenomic products, the Company does not expect to derive any significant
economic benefits from them until 2000.

     Remaining development efforts for the projects which are still incomplete
are highly complex and include the development and validation of the necessary
biochemistry, molecular biology and bioinformatic tools and information, as well
as small-scale deployment and commercial introduction. Funding for such projects
has been, and is expected to continue, from existing cash balances. The Company
estimates the costs to complete the remaining projects at approximately $111,000
for the remainder of 1999. Total costs to complete the projects from the date of
acquisition are estimated to be approximately $3.3 million.

     Although the Company has substantially completed three of the projects and
intends to complete the development of the remaining project and in-process
technologies, and although management believes in the likelihood of their
feasibility, there can be no assurance that such remaining project or in-process
technologies will be completed successfully, or that any of the in-process
technologies will achieve commercial success. If, at a later date, the Company
decides to no longer pursue one or all of these technologies, decides to
indefinitely postpone the research effort related to one or all of the
technologies, or determines that the discounted expected cash flows will no
longer meet projections in the aggregate, it will disclose that fact to
investors--explaining why it will not pursue commercialization or why the
research has been postponed (and when the research is expected to resume) and
how much of the purchase price the technologies (or projects) represent. If
these technologies are not successfully developed or commercially successful,
future results of operations of the Company may be adversely affected.
Additionally, the value of other intangible assets acquired may become impaired.

     Descriptions of the Company's estimates used to determine the value
assigned to the in-process technologies and costs, timing and anticipated
benefits of completing the development of the in-process technologies are
forward-looking statements that involve risks and uncertainties. The Company's
actual costs and timing to complete development of the remaining technologies
and any benefits derived therefrom or from completed technologies will depend on
many factors, including the Company's ability to complete development of the
remaining technologies successfully, to overcome remaining technical obstacles
and competing technologies, to gain market acceptance of products using such
technologies and to adapt to market developments and the availability to the
Company of adequate capital resources to commercialize such technologies. If the
Company is unsuccessful in developing or commercializing such technologies, the
Company will not achieve the benefits expected from acquiring such technologies
or obtain a return on its investment in connection with the acquisition and
would likely discontinue its operations with respect to such technologies.
Additionally, even if successfully completed, these projects will require
maintenance research and development after they have reached a state of
technological and commercial feasibility.





                                       11.
<PAGE>   12

RESULTS OF OPERATIONS

     Three Months and Nine Months Ended September 30, 1999 and 1998

     Revenues increased to $4.2 million and $13.5 million for the three and nine
months ended September 30, 1999, respectively, from $2.7 million and $8.6
million for the same periods in 1998. The increase in revenues was the result of
the expansion of the Company's collaborations with Japan Tobacco and Procter &
Gamble in late 1998, offset partially by the timing of revenue recognized
under other existing collaborations.

     Research and development expenses increased to $7.0 million and $21.5
million for the three and nine months ended September 30, 1999, respectively,
from $4.1 million and $11.2 million for the same periods in 1998. The increase
of $2.9 million for the three months ended September 30, 1999 as compared to the
same period in 1998 was primarily attributable to approximate increases of
$900,000 in research agreement expenses and $800,000 in laboratory supplies. The
increase of $10.3 million for the nine months ended September 30, 1999 as
compared to the same period in 1998 was primarily attributable to approximate
increases of $4.2 million in research agreement expenses, $2.2 million in
personnel expenses, and $1.8 million in laboratory supplies. Both of these
increases primarily relate to the Company's efforts in building its GeneExpress
databases which started in 1999, expansion of its target discovery and
bioinformatics businesses to accommodate new and expanded collaborations, and
further development of its Flow-thru Chip(TM) program. The Company expects
research and development expenses to increase as the Company expands its
GeneExpress databases, maintains new and expanding target discovery
collaborations, and further develops the Flow-thru Chip.

     General and administrative expenses increased to $2.3 million and $6.1
million for the three and nine months ended September 30, 1999, respectively,
from $1.7 million and $5.0 million for the same periods in 1998. These costs
include the costs of corporate operations, finance and accounting, human
resources and other general operations. For the three and nine months ended
September 30, 1999 as compared to the same periods in 1998, the increases of
$662,000 and $1.1 million, respectively, were primarily attributable to
approximate increases of $200,000 and $800,000, respectively, in personnel
expenses and $300,000 for both periods in professional fees. These increases
primarily relate to the Company's expansion of its business development efforts,
marketing costs of new products, and other general costs necessary to support
the expansion of the Company's operations. The Company expects that general and
administrative expenses will increase as the Company expands its product lines
and its sales and marketing efforts.

     Amortization of goodwill was $381,000 and $1.1 million for the three and
nine months ended September 30, 1999, respectively, as a result of the
acquisition of Oncormed in September 1998.

     Acquired in-process research and development was $35.2 million for the
three and nine months ended September 30, 1998, respectively, as a result of the
non-recurring charge for the acquisition of Oncormed in September 1998.

     Net interest income decreased to $126,000 and $589,000 for the three and
nine months ended September 30, 1999, respectively, from $428,000 and $1.5
million for the same periods in 1998 primarily due to smaller cash and
investment balances as a result of funding the Company's operating losses
through September 30, 1999 and additional interest expense paid on equipment
loans.

LIQUIDITY AND CAPITAL RESOURCES

     From inception through September 30, 1999, the Company financed its
operations through the sale of equity securities, payments under collaborative
agreements, and equipment and tenant improvement financing. In connection with
its collaboration with Procter & Gamble, the Company holds a promissory note of
$500,000 that is due in December 1999. The Company has also obtained $471,000



                                       12.
<PAGE>   13

of capital lease financing and $6.3 million under equipment and tenant
improvement loans. As of September 30, 1999, the Company had approximately $16.6
million in cash and marketable securities, compared to $31.0 million as of
December 31, 1998.

     In connection with the acquisition of Oncormed, the Company acquired
in-process research and development, which is comprised of several technology
projects. The Company expects to spend approximately $3.3 million in total to
develop commercially viable products using such technologies and to begin to
generate revenues from them. Costs to complete the development of these
remaining technologies are estimated to be $111,000 for the remainder of 1999.
Funding for such efforts has been, and is expected to continue, from existing
cash balances. These estimates are subject to change, given the uncertainties of
the development process, and no assurance can be given that deviations from
these estimates will not occur.

     In connection with the acquisition of Oncormed, the Company recorded a
restructuring liability of approximately $1.6 million. The objective of the
restructuring plan was to eliminate redundant general and administrative
employees of Oncormed and terminate contracts that the Company deemed to have no
on-going economic value to the Company. The restructuring liability consisted of
$373,000 in costs associated with the involuntary termination of ten Oncormed
employees and approximately $1.2 million in contract termination costs. During
the three months ending September 30, 1999, the Company substantially completed
its restructuring activities.

     Net cash used in operating activities was $10.5 million for the nine months
ended September 30, 1999 compared to $7.7 million for the nine months ended
September 30, 1998. The Company has primarily used cash during 1999 and 1998 to
fund the Company's operating losses in addition to expenditures relating to
intangibles and other assets.

     During the nine months ended September 30, 1999 and 1998, the Company had
expenditures relating to intangibles and other assets of approximately $937,000
and $523,000, respectively. These expenditures were primarily for patent costs
and license fees. The Company amortizes such patent costs to research and
development expense over the useful life of the underlying patent upon its
issuance. License fees are amortized to research and development expense over
periods of approximately one to seventeen years. These expenditures are
necessary and are expected to increase as a result of continuing efforts to
protect the Company's intellectual property and to secure rights to current
technology.

     The Company's investing activities, other than sales, maturities and
purchases of available-for-sale securities, consisted of capital expenditures,
which totaled $2.8 million and $5.6 million for the nine months ended September
30, 1999 and 1998, respectively, and the issuance of promissory notes to three
officers of the Company totaling $750,000 during the nine months ended September
30, 1999. The decrease in capital expenditures from year to year was primarily
due to the funding of tenant improvements and furniture purchases in the first
quarter of 1998 relating to the completion of the Company's new facility. The
Company expects to have additional capital expenditures in the fourth quarter of
1999 as it expands its facility requirements and acquires laboratory and
computer equipment to support expanding research and development activities. The
Company's capital expenditures in 1999 are expected to be less than those in
1998.

     Net cash used in financing activities was $283,000 for the nine months
ended September 30, 1999 compared to net cash provided by financing activities
of $4.0 million in the nine months ended September 30, 1998. During the nine
months ended September 30, 1999, the Company obtained $425,000 to finance tenant
improvements compared to $4.3 million of equipment financing received during the
same period in 1998. The cash obtained in these periods was offset by increased
repayments under equipment loans and a capital lease obligation during 1999.

     In June 1998, the Company entered into a loan agreement for the financing
of laboratory, computer and office equipment. Under the loan agreement, the
Company may borrow up to $5.0 million




                                       13.
<PAGE>   14

through June 1999. At September 30, 1999, the Company had borrowed approximately
$4.8 million. The Company expects to extend the borrowing period and increase
the borrowing amount under the loan agreement or obtain similar financing from
additional sources during the fourth quarter of 1999.

     In January 1999, the Company entered into a three-year agreement with
Affymetrix, pursuant to which Affymetrix will supply its GeneChip probe arrays
to the Company for the development of gene expression databases. Under the terms
of the agreement, the Company will pay Affymetrix subscription fees for access
to the probe arrays, purchase the probe arrays and related instrumentation and
software, and pay royalties to Affymetrix on revenues generated from certain
database subscriptions fees. The Company's commitments under other research and
license agreements do not represent a significant expenditure in relation to the
Company's total research and development expense.

     In September 1999, the Company renegotiated certain elements of its
existing Genomic Database Collaboration and License Agreement with N.V. Organon.
As amended, the agreement permits Organon to terminate the collaboration on
February 27, 2000 upon payment of a specified amount to the Company. In the
event that Organon elects early termination at that time, the Company would
purchase rights to data valuable for its GeneExpress databases.

     To date, all revenue received by the Company has been generated principally
from its collaborations. The Company expects that substantially all revenue for
the foreseeable future will come from collaborative partners and subscriptions
to its GeneExpress databases. Furthermore, the Company's ability to achieve
profitability will be dependent upon the ability of the Company to enter into
additional collaborations and successfully commercialize its GeneExpress
databases. There can be no assurance that the Company will be able to negotiate
additional collaborations in the future on acceptable terms, if at all, or that
current or future collaborations will be successful and provide the Company with
expected benefits or that the Company will be able to successfully commercialize
its GeneExpress databases.

     The Company believes that existing cash and marketable securities and
anticipated cash flow from its current collaborations will be sufficient to
support the Company's operations at least through the middle of the year 2000.
The estimate for the period for which the Company expects its available cash
balances and estimated cash flow from its current collaborations to be
sufficient to meet its capital requirements is a forward-looking statement that
involves risks and uncertainties. The Company's actual future capital
requirements and the adequacy of its available funds will depend on many
factors, including progress of its discovery programs, the number and breadth of
these programs, the ability of the Company to establish and maintain additional
collaboration and licensing arrangements, the commercial success of the
in-process technologies acquired in the acquisition of Oncormed and the progress
of the development and commercialization efforts of the Company's collaborative
partners. These factors also include the level of the Company's activities
relating to its independent discovery programs and to the development and
commercialization rights it retains in its collaboration arrangements, competing
technological and market developments, the costs associated with obtaining
access to tissue samples and related information and the costs involved in
preparing, filing, prosecuting, maintaining and enforcing patent claims and
other intellectual property rights. The Company expects that it will require
significant additional financing in the future, which it may seek to raise
through public or private equity offerings, debt financing or additional
collaboration and licensing arrangements. No assurance can be given that
additional financing or collaboration and licensing arrangements will be
available when needed, if at all, or that, if available, will be obtained on
terms favorable to the Company and its stockholders. To the extent that the
Company raises additional capital by issuing equity or convertible debt
securities, ownership dilution to stockholders will result. If adequate
financing is not available when needed, the Company may be required to curtail
significantly one or more of its research and development programs or to obtain
funds through arrangements with collaborative partners or others that may
require the Company to relinquish rights to certain of its technologies,
discoveries or potential products, or to grant licenses on terms that are not
favorable to the Company, any of which could have a material adverse effect on
the Company's business, financial condition and results of operations. In the
event that adequate funds are not available, the Company's business would be
adversely affected.





                                       14.
<PAGE>   15

YEAR 2000 COMPLIANCE

     Many computer systems and software products are coded to accept two digit
entries in the date code field. These date code fields will need to accept four
digit entries to distinguish 21st century dates from 20th century dates. As a
result, at the end of this year, computer systems and software used by many
companies may need to be upgraded to comply with such "Year 2000" requirements.
The Company uses a significant number of computer software programs and
operating systems in connection with its database products, services and
internal operations. Such software and systems were purchased and installed with
a view towards Year 2000 compliance. Nevertheless, Year 2000 problems could
affect the Company's research and development, financial, administrative and
communication operations.

     The Company has implemented a program designed to address Year 2000
problems. A cross-functional Year 2000 project team has performed a
comprehensive review of internal computer systems, electronic devices and
software, and identified material third parties which the Company relies upon
for its operations.

     In October 1999, the Company substantially completed its compliance audits
and Year 2000 validation testing on its internal computer systems, electronic
devices and software, noting that systems critical to the Company's business
that were not Year 2000 compliant have been, or are in the process of being,
replaced or corrected as identified through programming modifications and/or
software upgrades.

     The Company has also evaluated the status of Year 2000 compliance of third
parties with whom the Company has material relationships through Year 2000
surveys and review of public documents and third-party web sites. As a result,
the Company has determined that the majority of such third parties represent
being compliant with regards to Year 2000 while the remainder are still in
the process of becoming Year 2000 compliant. The Company will continue to
monitor their progress.

     The Company expects to complete its Year 2000 efforts in the fourth quarter
of 1999. As the Company completes its overall assessments of its Year 2000
requirements, it will develop and implement, if necessary, appropriate
contingency plans to mitigate, to the extent possible, the effects of Year 2000
noncompliance on the Company's operations. The preceding discussion, including
the estimated timing of completion of these efforts, includes forward-looking
statements that involve risk and uncertainties, including the risk that such
efforts will not adequately address such Year 2000 problems, the risk that
third-party assurances regarding Year 2000 compliance are inaccurate or
incomplete, and the risk that the Company will not be able to successfully
implement its contingency plans in a timely manner. If any of these
circumstances occur, the Company's business will be adversely affected.

     External and internal costs specifically associated with modifying internal
software for Year 2000 compliance are expensed as incurred. To date, costs have
not been material and are not expected to be material in the future. Such costs
do not include normal system upgrades and replacements. Based on the Company's
current plans and efforts to date, the Company believes that changes mandated by
the Year 2000 issues will not cause any material adverse effects on the
Company's business, financial condition and results of operations. There is no
guarantee, however, that all problems will be foreseen and corrected, or that no
material disruption of the Company's business will occur.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURE ABOUT MARKET RISK

     The Company does not hold any financial instruments subject to significant
market risk.

PART II   OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS

     On October 19, 1999 a lawsuit was filed in the Circuit Court of Cook
County, Illinois against Oncormed, Inc. and Gene Logic Inc. alleging that
Oncormed was negligent in determining and reporting laboratory test results of a
genetic test conducted by Oncormed.




                                       15.
<PAGE>   16

Oncormed sold its testing business to a third-party company prior to its
acquisition by Gene Logic. The Company is not engaged in any type of genetic
testing, nor has it plans to enter such markets. The Company maintains the
usual and customary protection against such claims and does not believe this
action will have a material adverse impact on the Company.

ITEM 2. CHANGES IN SECURITIES AND USE OF PROCEEDS

        None.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

        None.

ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

        None.

ITEM 5. OTHER INFORMATION

        None.

ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K


         A)    EXHIBITS:

               *10.55       Executive Severance Plan, adopted March 19, 1999

               ++++10.56    First Amendment to Genomic Database Collaboration
                            and License Agreement, executed September 1999,
                            between Registrant and N.V. Organon

               ++++10.57    Letter Agreement, dated September 28, 1999, between
                            Registrant and Japan Tobacco, Inc.

               11.1         Statement regarding computation of net loss per
                            share

               27.1         Financial Data Schedule

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

               *            Indicates management compensatory plan, contract or
                            arrangement.

               ++++         Confidential treatment has been requested with
                            respect to certain portions of this exhibit.
                            Omitted portions have been filed separately with the
                            Securities and Exchange Commission.

         B)    REPORTS ON FORM 8-K:

               No reports on Form 8-K were filed during the three months ended
               September 30, 1999.




                                       16.
<PAGE>   17




                                   SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.

                                 GENE LOGIC INC.


Date:   November 15, 1999       By: /s/ Michael J. Brennan, M.D., Ph.D.
                                    --------------------------------------
                                    Michael J. Brennan, M.D., Ph.D.
                                    Chief Executive Officer and Director
                                    (Principal Executive Officer)

Date:   November 15, 1999       By: /s/ Philip L. Rohrer, Jr.
                                    --------------------------------------
                                    Philip L. Rohrer, Jr.
                                    Chief Financial Officer
                                    (Principal Financial and Accounting Officer)




                                       17.