<PAGE>   1

                       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, 1996.

      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:  0-19749

                             CHEMTRAK INCORPORATED

             Delaware                                77-0295388
-------------------------------          -------------------------------
(State or other jurisdiction of        (I.R.S Employer Identification No.) 
incorporation or organization)

                   929 E. Arques Avenue, Sunnyvale, CA  94086
                   ------------------------------------------
                    (Address of principal executive offices)

      Registrant's telephone number, including area code:  (408) 773-8156

          Securities registered pursuant to Section 12(g) of the Act:

                          Common Stock $.001 par value
                          ----------------------------
                                (Title of 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 the number of shares outstanding of each of the issuer's
classes of common stock, as of the latest practicable date.

Class: Common Stock $.001 par value  Outstanding at October 31, 1996: 10,786,063
<PAGE>   2
                             CHEMTRAK INCORPORATED
                                     INDEX



<TABLE>
<S>              <C>                                                                                       <C>              <C>
PART I.          FINANCIAL INFORMATION                                                                     PAGE
                                                                                                           ----
                                                                                                             NO.
                                                                                                             ---

                 Item 1:  Financial Statements

                 Condensed Balance Sheets as of September 30, 1996 and December 31, 1995                        3

                 Condensed Statements of Operations for the three and nine months ended
                 September 30, 1996 and 1995                                                                    4

                 Condensed Statements of Cash Flows for the nine months ended
                 September 30, 1996 and 1995                                                                    5

                 Notes to Condensed Financial Statements                                                      6-7

                 Item 2:  Management's Discussion and Analysis of Financial Condition
                 and Results of Operations                                                                   8-10


PART II.         OTHER INFORMATION

                 Item 6:  Exhibits and Reports on Form 8-K                                                    11


SIGNATURES                                                                                                    12


EXHIBITS                                                                                                   13-14


</TABLE>
<PAGE>   3
                             CHEMTRAK INCORPORATED
                            CONDENSED BALANCE SHEETS



<TABLE>
<CAPTION>
                                          ASSETS
                                                              September 30, 1996          December 30, 1996
                                                              ------------------         ------------------
                                                                 (unaudited)
<S>                                                               <C>                       <C>
Current assets:
   Cash and cash equivalents                                       $   4,672,000              $   4,251,000
   Short-term investments                                              1,489,000                  2,003,000
   Accounts receivable, net                                              457,000                    136,000
   Inventories                                                           382,000                    434,000
   Prepaid expenses and other current assets                             375,000                    245,000
                                                                   -------------              -------------    
      Total current assets                                             7,375,000                  7,069,000
   Property and equipment, net                                         2,894,000                  3,248,000
   Other assets                                                           66,000                     66,000
                                                                   -------------              -------------
Total assets                                                       $  10,335,000              $  10,383,000
                                                                   =============              =============


                           LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
   Accounts payable                                                $     321,000              $     632,000
   Accrued payroll and benefits                                          215,000                    121,000
   Other accrued liabilities                                             600,000                    258,000
   Accrued royalties                                                     131,000                    114,000
                                                                   -------------              -------------    
      Total current liabilities                                        1,267,000                  1,125,000

Accrued rent                                                             281,000                    240,000

Convertible debentures                                                 3,387,000                          0

Stockholders' equity:
   Common stock                                                           11,000                     10,000
   Additional paid-in capital                                         39,422,000                 37,528,000
   Deferred compensation                                                 (54,000)                   (38,000)
   Accumulated deficit                                               (33,979,000)               (28,482,000)
                                                                   -------------              -------------    
      Total stockholders' equity                                       5,400,000                  9,018,000
                                                                   -------------              -------------    
Total liabilities and stockholders' equity                         $  10,335,000              $  10,383,000
                                                                   =============              =============    
</TABLE>





  See accompanying notes.
<PAGE>   4


                             CHEMTRAK INCORPORATED
                       CONDENSED STATEMENTS OF OPERATIONS
                                  (unaudited)



<TABLE>
<CAPTION>
                                                                Three months ended                      Nine months ended
                                                                   September 30,                           September 30,
                                                      ----------------------------------      ----------------------------------
                                                             1996                 1995               1996              1995
                                                      ----------------  ----------------      ----------------  ----------------
<S>                                                  <C>                <C>                  <C>                  <C>
Net revenues:
    Product sales                                    $      583,000     $        271,000     $    2,020,000       $    1,935,000
    Funded research and other revenues                         ----              215,000            175,000            1,125,000
                                                      -------------        -------------      -------------        ------------- 
        Total net revenues                                  583,000              486,000          2,195,000            3,060,000

Cost and expenses:
    Cost of product sales                                   920,000              518,000          2,475,000            2,555,000
    Research and development                                447,000              807,000          1,920,000            2,057,000
    Marketing, general and administrative                 1,064,000              465,000          3,337,000            1,892,000
    Purchase of in-process research and development            ----                 ----               ----            1,500,000
                                                      -------------        -------------      -------------        ------------- 

        Total costs and expenses                          2,431,000            1,790,000          7,732,000            8,004,000
                                                      -------------        -------------      -------------        ------------- 
Operating loss                                           (1,848,000)          (1,304,000)        (5,537,000)          (4,944,000)

Net other income and expense                                (20,000)              63,000             40,000              221,000
                                                      -------------        -------------      -------------        ------------- 
Net Income (loss)                                     $  (1,868,000)       $  (1,241,000)     $  (5,497,000)       $  (4,723,000)
                                                      =============        =============      =============        ============= 
Net income (loss) per share                           $       (0.18)       $       (0.13)     $       (0.56)       $       (0.49)
                                                      =============        =============      =============        ============= 

Shares used in calculating per share amounts             10,192,000            9,699,000          9,808,000            9,624,000
                                                      =============        =============      =============        ============= 
</TABLE>









                              See accompanying notes.




                                       4
<PAGE>   5
                             CHEMTRAK INCORPORATED
                       CONDENSED STATEMENTS 0F CASH FLOWS
                Increase (decrease) in cash and cash equivalents
                                  (unaudited)

<TABLE>
<CAPTION>
                                                                                     Nine months ended
                                                                                       September 30,
                                                                        -------------------------------------
                                                                               1996                1995
                                                                        -----------------   -----------------     
<S>                                                                     <C>                  <C>
Operating activities:
   Net loss                                                             $   (5,497,000)      $     (4,723,000)
   Adjustment to reconcile net loss to net cash and
     cash equivalents used in operating activities:
       Depreciation and amortization                                           641,000                639,000
       Accrued rent                                                             41,000                 41,000
       Stock option compensation and other                                       2,000                (29,000)
       Purchase of in-process research and development for
           common stock                                                              0                900,000
   Changes in operating assets and liabilities:
       Accounts receivable                                                    (321,000)               417,000
       Inventories                                                              52,000                412,000
       Prepaid expenses and other current assets                              (130,000)               156,000
       Accounts payable                                                       (311,000)              (258,000)
       Accrued payroll and benefits                                             94,000               (365,000)
       Other accrued liabilities                                               359,000                (14,000)
                                                                     -----------------      -----------------     
            Net cash and cash equivalents provided
              by (used in) operating activities                             (5,070,000)            (2,824,000)
                                                                     -----------------      -----------------     

Investing activities:
   Proceeds from available-for-sale securities                                 514,000              2,492,000
   Aquisition of property and equipment, net                                  (287,000)              (347,000)
                                                                     -----------------      -----------------     
            Net cash and cash equivalents provided
             by (used in) investing activities                                 227,000              2,145,000
                                                                     -----------------      -----------------     
Financing activities:
   Issuance of Convertible Debentures                                        5,000,000                      0
   Proceeds from issuance of common stock                                      264,000                145,000
                                                                     -----------------      -----------------     
            Net cash and cash equivalents provided
             by financing activities                                         5,264,000                145,000
                                                                     -----------------      -----------------     
Net increase (decrease) in cash and cash equivalents                           421,000               (534,000)
Cash and cash equivalents at beginning of period                             4,251,000              2,280,000
                                                                     -----------------      -----------------     
Cash and cash equivalents at end of period                            $      4,672,000       $      1,746,000
                                                                     =================      =================     
</TABLE>





                             See accompanying notes.




                                       5
<PAGE>   6

                             CHEMTRAK INCORPORATED

                    NOTES TO CONDENSED FINANCIAL STATEMENTS

                               September 30, 1996

                                  (unaudited)

Note 1.  Basis of Presentation

         The accompanying unaudited financial statements include all
adjustments consisting of normal recurring adjustments which the Company's
management believes to be necessary to fairly present the Company's financial
position as of September 30, 1996, and the results of operations for the three
and nine month periods ended September 30, 1996 and 1995.

         The operating results of the interim periods presented are not
necessarily indicative of the results for the full year.  The accompanying
financial statements should be read in conjunction with the financial
statements for the year ended December 31, 1995, included in the ChemTrak
Incorporated Annual Report on Form 10-K for the fiscal year ended December 31,
1995 (the "Form 10-K").  The information set forth in the accompanying balance
sheet as of December 31, 1995, has been derived from the audited balance sheet
included in the above-referenced Form 10-K and Annual Report.

Note 2.  Convertible Debentures

         In May 1996 the Company issued $5,000,000 principal amount of
Convertible Debentures due May 1998.  These debentures are convertible into the
Common Stock of the Company according to a formula based on the market price of
the shares at the time of conversion.  As of September 30, 1996,  758,710
shares of Common Stock had been issued upon conversion of the debentures.  As
of October 31, 1996, an additional 156,347 shares had been issued in respect of
conversions. As of October 31, 1996, a total of 45,923 shares of Common Stock
were issued in lieu of interest to the holders of the Debentures.

Note 3.  Net Loss Per Share

         Net loss per share is computed using the weighted number of shares
outstanding. Common equivalent shares from stock options are excluded in the
computation as their effect is antidilutive.




                                       6
<PAGE>   7
Note 4.  Inventories

         Inventories are stated at the lower of standard cost (which
approximates actual costs on a first-in, first-out basis) or market.
Inventories consisted of the following:

<TABLE>
<CAPTION>
                                                              September 30, 1996          December 31,1995
                                                              ------------------         ------------------
<S>                                                           <C>                        <C>                   
Raw materials......................................           $        100,000            $        145,000
Work in process....................................                     61,000                      41,000
Finished goods.....................................                    221,000                     248,000
                                                             -----------------           -----------------     

        Total......................................          $         382,000            $        434,000
                                                             =================           =================     
</TABLE>












                                       7
<PAGE>   8

                             CHEMTRAK INCORPORATED

               MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                      CONDITION AND RESULTS OF OPERATIONS


         Except for the historical information contained herein, the following
discussion contains forward-looking statements that involve risks and
uncertainties.  The Company's actual results could differ materially from those
discussed here.  Factors that could cause or contribute to such differences
include, but are not limited to, those discussed in this section, as well as in
the Company's Form 10-K for the year ended December 31, 1995.

OVERVIEW

         In December 1995 ChemTrak regained the exclusive rights to market its
AccuMeter Cholesterol Self-Test in the United States retail market.  Previously
sold as the Advanced Care Cholesterol Test by Direct Access Diagnostics
("DAD"), a Johnson & Johnson company, it has been relaunched under the trade
name CholesTrak.  CholesTrak is the first and only over-the-counter cholesterol
test to be cleared by the U.S. Food and Drug Administration (the "FDA").

         On April 29, 1996, the Company announced it had signed a multi-year
distribution agreement with Helena Laboratories (Canada) Ltd. for its
CholesTrak home cholesterol test.  This agreement will result in the launch of
CholesTrak for the first time in Canada.  The Company began shipping to Helena
Laboratories on September 30, 1996.

         On July  2, 1996, the Company announced it had received marketing
clearance from the  U.S. FDA for its H. pylori test for use in physicians
offices.  In March 1995, ChemTrak entered into an exclusive distribution and
supply agreement for its H. pylori test in the U.S.  market with Astra Merck,
Inc. ("Astra Merck") a major pharmaceutical company.  The Company expects to
begin shipping H. pylori tests in the fourth quarter, 1996.

         The Company has several products currently in development, some of
which are based on the AccuMeter technology.  Other product applications have
only reached the laboratory feasibility stage.  Factors that affect the
Company's success include ChemTrak's ability to develop future products, its
ability to manufacture its products, obtain regulatory clearance for marketing
its products, and have its products marketed successfully, all on a timely
basis.  There can be no assurance that the Company's current product
development efforts will be successfully completed, that products will be
manufactured in the required commercial quantities, that timely required
clearances will be obtained for the Company's future products on a timely
basis, if at all, or that the Company's products will be marketed successfully.







                                       8
<PAGE>   9
         As of September 30, 1996 the Company had an accumulated deficit of
$33,979,000.  Profitability is highly dependent upon numerous factors
including, but not limited to, the Company's ability to provide product in
sufficient, cost effective quantities and the ultimate success of its products
in the U.S. over-the-counter market.  Due to the uncertainty of these factors,
it is difficult to reliably predict when such profitability may occur, if at
all.

         The Company has historically experienced significant fluctuations in
its operating results and anticipates that these fluctuations may continue.
The market price of the shares of the Company's common stock, like those of
other emerging medical technology companies, has been highly volatile.  Various
factors, including but not limited to fluctuations in the Company's operating
results, technical and regulatory developments, general market and economic
factors, may have a significant effect on the market price of the Company's
common stock.

RESULTS OF OPERATIONS

NET REVENUES

         Total net revenues increased to $583,000 for the three months ended
September 30, 1996 from $486,000 for the three months ended September 30, 1995.
Product sales increased to $583,000 in the three months ended September 30,
1996 from $271,000 in the three months ended September 30, 1995, due to the
relaunch of the Company's AccuMeter Cholesterol Self-Test under the trade name
CholesTrak.  The Company did not have any funded research for the three months
ended September 30, 1996 compared to $215,000 for the three months ended
September 30, 1995.  The funded research of $215,000 for the third quarter of
1995 was a milestone payment from DAD for completion of the fourth phase of a
second generation total cholesterol test.  For the nine months ended September
30, 1996, net revenue decreased to $2,195,000 as compared to $3,060,000 for the
nine months ended September 30, 1995.  During the nine months ended September
30, 1996, product sales were $2,020,000 as compared to $1,935,000 for the nine
months ended September 30, 1995.  Funded research was $175,000 for the nine
months ended September 30, 1996, compared with $1,125,000 for the nine months
ended September 30, 1995.  This decrease was due to reduced milestone payments
from Astra Merck and DAD.

COST OF PRODUCT SALES

         For the three months ended September 30, 1996, the cost of product
sales increased to $920,000 from $518,000 for the three months ended September
30, 1995.  The increase was due to the increase in product sales volume.  The
decrease in cost of product sales for the nine months ended September 30, 1996
to $2,475,000 from $2,555,000 for the same period last year is primarily due to
improved manufacturing efficiencies.

         Product gross margin as a percentage of product sales increased to a
negative 58% for the three months ended September 30, 1996 from a negative 91%
for the same period in 1995.  Product gross margin as a percentage of sales
increased to a negative 23% for the nine months ended September 30, 1996 from a
negative 32% for the nine months ended September 30, 1995.  These improvements
were due to successful efforts made by the company to decrease manufacturing
costs.





                                       9
<PAGE>   10
RESEARCH AND DEVELOPMENT

         Research and development expenses decreased to $447,000 in the three
months ended September 30, 1996 from $807,000 for the three months ended
September 30, 1995.  For the nine months ended September 30, 1996, research and
development expenses decreased to $1,920,000 from $2,057,000 for the nine
months ended September 30, 1995.  These decreases were primarily due to
decreased research spending associated with the Company's H. Pylori test, which
received FDA approval early in the third quarter of 1996.

MARKETING, GENERAL AND ADMINISTRATIVE

         Marketing, general and administrative expenses increased to $1,064,000
for the three months ended September 30, 1996 from $465,000 for the three
months ended September 30, 1995.  For the nine months ended September 30, 1996,
marketing, general and administration expenses were $3,337,000 as compared to
$1,892,000 for the nine months ended September 30, 1995.  These increases were
primarily due to selling and advertising expenses associated with the relaunch
of the Company's CholesTrak total cholesterol test.

INTEREST INCOME AND EXPENSE

         Interest income and expense decreased to $20,000 net expense in the
three months ended September 30, 1996 from $63,000 income for the three months
ended September 30, 1995, and decreased to $40,000 income for the nine months
ended September 30, 1996 from $221,000 income for the nine months ended
September 30, 1995.  These decreases were due to reduced levels of short term
investments and interest expense on convertible debentures that the Company
issued during May 1996.

LIQUIDITY AND CAPITAL RESOURCES

         At September 30, 1996, the Company had approximately $6,161,000 in
cash and short-term investments.

         In May 1996, the Company issued $5,000,000 principal amount of
Convertible Debentures due May 1998, raising approximately $4,700,000 net of
issuance costs.  Prior to this issuance, the Company had no long-term debt.
The debentures bear interest at an annual rate of 7.5% which is payable in cash
or the Company's Common Stock, at the option of the Company.  The debentures
are convertible into the Company's Common Stock according to a formula based on
the market price at the time of conversion.  As a result of conversions through
September 30, 1996 the principal amount of debentures outstanding has been
reduced to $3,387,000.

         The Company believes that its existing capital resources, together
with internally generated funds, will be sufficient to meet its operating needs
as well as its purchase requirements for property, plant and equipment for at
least the next twelve months.





                                       10
<PAGE>   11
                             CHEMTRAK INCORPORATED

                          PART II.  OTHER INFORMATION

<TABLE>
<S>         <C>                                                            <C>
Item 6.     Exhibits and Reports on Form 8-K                               Page

            a)   Exhibits

                 11.1       Statement re: computation of income 
                            (loss) per share                                13

                 27.1       Financial Data Schedule                         14

            b)   Reports on Form 8-K

                 None

</TABLE>









                                       11
<PAGE>   12


                             CHEMTRAK INCORPORATED

                                   SIGNATURES

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




Date:    November 12, 1996               CHEMTRAK INCORPORATED


                                          /s/ Prithipal Singh, Ph.D.
                                          -------------------------------------
                                          Prithipal Singh, Ph.D.
                                          Chief Executive Officer and
                                          Chairman of the Board
                                          (Principal Executive Officer)



                                          /s/ Edward F. Covell
                                          -------------------------------------
                                          Edward F. Covell
                                          President and Chief Operating Officer
                                          (Principal Financial Officer)


                                           /s/ Douglas W. Lange
                                           ------------------------------------
                                           Douglas W. Lange
                                           Principal Accounting Officer






                                       12
<PAGE>   13
                                Exhibit Index


                 11.1       Statement re: computation of income 
                            (loss) per share                                

                 27.1       Financial Data Schedule