<PAGE>   1
                UNITED STATES SECURITIES AND EXCHANGE COMMISSION

                              Washington, DC 20549

                                   FORM 10-QSB

[X]  QUARTERLY REPORT UNDER SECTION 13 OF THE SECURITIES EXCHANGE ACT OF 1934

                      FOR THE QUARTER ENDED MARCH 31, 1999

                                       OR

[ ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
                                 EXCHANGE ACT

              For the transition period from ________ to _________

                         COMMISSION FILE NUMBER 1-14004

                                XENOMETRIX, INC.
        (Exact name of small business issuer as specified in its charter)

           DELAWARE                                            04-3166089
(State or other jurisdiction of                               (IRS employer
incorporation or organization)                            identification number)


                             2425 NORTH 55TH STREET
                                BOULDER, CO 80301
                    (Address of principal executive offices)


                                 (303) 447-1773
                           (Issuers telephone number)


   Check whether issuer (1) filed all reports required to be filed by Section 13
or 15(d) of the Exchange Act during the past 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
                                 -----        -----

   State the number of shares outstanding of each of the issuer's classes of
common equity, as of the latest practicable date.

COMMON STOCK, $0.001 PAR VALUE                        2,948,135 COMMON SHARES
           (Class)                                 OUTSTANDING AT MARCH 31, 1999


   Transitional Small Business Disclosure Format    Yes      No    X 
                                                       -----     -----      

                                       1

<PAGE>   2



                                 XENOMETRIX, INC
                                   FORM 10-QSB
                       FOR THE PERIOD ENDED MARCH 31, 1999

                                      INDEX


<TABLE>
<S>      <C>                                                                                              <C>
PART I - FINANCIAL INFORMATION

Item 1.  Financial Statements

         Balance Sheet - March 31, 1999...................................................................Page  3

         Statement of Operations - Quarters ended March 31, 1999 and 1998.................................Page  4

         Statement of Cash Flows - Quarters ended March 31, 1999 and 1998.................................Page  5

         Notes to Financial Statements....................................................................Page  6

Item 2.  Management's Discussion and Analysis of Financial Condition and
            Results of Operations.........................................................................Page  8



PART II - OTHER INFORMATION


Item 6.  Exhibits.........................................................................................Page 12

Signatures................................................................................................Page 13
</TABLE>


                                       2

<PAGE>   3


Part One--Financial Information

                                XENOMETRIX, INC.
                                  Balance Sheet
                                 March 31, 1999
                                   (Unaudited)

                                     Assets

<TABLE>
<S>                                                                                    <C>
Current Assets:
     Cash                                                                                      $  85,000
     Accounts receivable, net                                                                     82,000
     Inventory                                                                                    13,000
     Prepaid insurance                                                                            38,000
     Deposits and prepaid expense                                                                 88,000
                                                                                             -----------
             Total current assets                                                                306,000

Property and equipment, net                                                                      501,000
Patents, net                                                                                     401,000
             Total assets                                                                    $ 1,208,000
                                                                                             ===========

                                  Liabilities and Stockholders' Equity

Current Liabilities:
     Accounts payable                                                                        $   374,000
     Accrued royalties                                                                           202,000
     Accrued salaries and wages                                                                  166,000
     Other accrued liabilities                                                                    83,000
     Senior promissory notes                                                                     284,000
                                                                                             -----------
             Total current liabilities                                                         1,109,000
                                                                                             -----------

Stockholders' Equity:
Preferred stock--$.001 par value; 5,000,000 shares authorized;
     no shares issued and outstanding                                                                  -
Common stock--$.001 par value; 20,000,000 shares authorized;
     2,948,000 shares issued and outstanding                                            
                                                                                                   3,000
Additional paid-in capital                                                                    16,093,000
Accumulated deficit                                                                          (15,997,000)
             Total stockholders' equity                                                           99,000
                                                                                             -----------
             Total liabilities and stockholders' equity                                      $ 1,208,000
                                                                                             ===========
</TABLE>


   The accompanying notes are an integral part of these financial statements.

                                       3

<PAGE>   4




                                XENOMETRIX, INC.
                             Statement of Operations
                                 March 31, 1999
                                   (Unaudited)

<TABLE>
<CAPTION>
                                                        Quarter Ended                    Nine Months Ended
                                                          March 31,                          March 31,
                                                          ---------                          ---------
                                                   1999               1998             1999             1998
                                                   ----               ----             ----             ----
<S>                                             <C>               <C>                <C>             <C> 
Revenue:
     Products and services                       $   93,000        $  103,000        $  323,000      $   497,000
     Licensing revenue                            1,926,000                 -         2,552,000                -
                                                 ----------        ----------        ----------      -----------
     Total revenue                                2,019,000           103,000         2,875,000          497,000

Cost of revenue:
     Cost of products and services                  103,000           114,000           384,000          418,000
     Cost of licensing revenue                      237,000                 -           368,000                -     
                                                 ----------        ----------        ----------      -----------
     Total cost of revenue                          340,000           114,000           752,000          418,000
                                                 ----------        ----------        ----------      -----------
         Gross profit                             1,679,000           (11,000)        2,123,000           79,000
                                                 ----------        ----------        ----------      -----------
Research and development                             54,000           234,000           279,000          946,000
Selling, general and administrative                 187,000           484,000           910,000        1,468,000
                                                 ----------        ----------        ----------      -----------
     Total operating expense                        241,000           718,000         1,189,000        2,414,000
                                                 ----------        ----------        ----------      -----------
Operating income (loss)                           1,438,000          (729,000)          934,000       (2,335,000)
     Interest expense, net                          (35,000)         (290,000)         (233,000)        (567,000)
                                                 ----------        ----------        ----------      -----------
Net income (loss)                                $1,403,000        $(1,019,000)      $  701,000      $(2,902,000)
                                                 ==========        ===========       ==========      ===========

Income (loss) per common share-basic             $     0.48        $     (0.35)      $     0.24      $     (0.98)
                                                 ==========        ===========       ==========      ===========

Income (loss) per common share-diluted           $     0.44        $     (0.35)      $     0.24      $     (0.98)
                                                 ==========        ===========       ==========      ===========

Weighted average shares outstanding               2,948,000          2,948,000        2,948,000        2,948,000
                                                 ==========        ===========       ==========      ===========

Weighted & dilutive potential average shares      3,190,000                  -        2,954,000                -
                                                 ==========        ===========       ==========      ===========
</TABLE>




   The accompanying notes are an integral part of these financial statements.


                                       4
<PAGE>   5




                             Statement of Cash Flows
                                   (Unaudited)

<TABLE>
<CAPTION>
                                                                                       Nine Months Ended
                                                                                            March 31
                                                                              -------------------------------------
                                                                                    1999                1998
                                                                              ------------------  -----------------
<S>                                                                                 <C>              <C>
Cash Flows from Operating Activities:
       Net  income (loss)                                                            $  701,000       $ (2,902,000)
       Adjustments to reconcile net loss to net cash
       used in operating activities:
             Depreciation and amortization                                              271,000            264,000
             Amortization of discount on senior promissory notes                        105,000            412,000
             Changes in assets and liabilities:
                  Accounts receivable                                                    33,000            187,000
                  Receivable from termination of operating lease                              -            115,000
                  Inventory                                                              42,000             20,000
                  Prepaid insurance                                                     143,000             82,000
                  Deposits and prepaid expense                                          (36,000)            31,000
                  Accounts payable and accrued liabilities                             (120,000)           172,000
                  Deferred revenue                                                            -            251,000
                                                                                 --------------       ------------
             Net cash provided by (used in) operating activities                      1,139,000         (1,368,000)
                                                                                 --------------       ------------

Cash Flows from Investing Activities:
       Capital expenditures                                                                   -            (17,000)
       Patent acquisition cost                                                         (179,000)           (79,000)
                                                                                 --------------       ------------
             Net cash used in investing activities                                     (179,000)           (96,000)
                                                                                 --------------       ------------

Cash Flows from Financing Activities:
       Repayment of senior promissory notes                                          (1,216,000)                 -
       Proceeds from issuance senior promissory notes and warrants                            -          1,000,000
                                                                                 --------------       ------------
             Net cash provided by financing activities                               (1,216,000)         1,000,000
                                                                                 --------------       ------------

Net increase (decrease) in cash                                                        (256,000)          (464,000)

Cash and cash equivalents at beginning of period                                        341,000            603,000
                                                                                 --------------       ------------

Cash and cash equivalents at end of period                                         $     85,000        $   139,000
                                                                                 ==============       ============
</TABLE>




   The accompanying notes are an integral part of these financial statements.


                                       5
<PAGE>   6



                                XENOMETRIX, INC.
                          NOTES TO FINANCIAL STATEMENTS
                      FOR THE PERIOD ENDING MARCH 31, 1999
                                   (Unaudited)

1.       Basis of Presentation

The accompanying financial statements are unaudited. However, in the opinion of
management, the accompanying financial statements reflect all adjustments,
consisting of only normal recurring adjustments, necessary for fair
presentation. Interim results of operations are not necessarily indicative of
results for the full year. These financial statements should be read in
conjunction with the Xenometrix Annual Report on Form 10-KSB for the year ended
June 30, 1998.

Except for the historical information contained in this Form 10-QSB, this Form
contains forward-looking statements that involve risks and uncertainties.
Xenometrix's actual results could differ materially from those discussed in this
Report. Factors that could cause or contribute to such differences include, but
are not limited to, those discussed in this Report and any documents
incorporated herein by reference, as well as in the Xenometrix Annual Report on
Form 10-KSB for the year ended June 30, 1998.

2.  Senior Promissory Notes

Between June 20, 1997 and January 12, 1998, Xenometrix issued Senior promissory
notes, (the "Notes") in the total amount of $1,500,000 to serve as bridge
financing. The Notes are collateralized by a security interest in all of the
assets of the Company. The Notes were originally due March 25, 1998. The
maturity date on the Notes has been extended several times, most recently until
June 15, 1999. The Notes bear interest at 12% per annum. In the event of a sale
of the Company prior to the maturity date, the Notes are due at the closing of
such sale. In connection with the issuance of these Notes, Xenometrix issued
warrants to purchase 499,995 shares of common stock. In consideration for the
extension of the due date on the Notes to February 25, 1999, the exercise price
of the warrants was reduced to $0.125 per share and the Company agreed to
continue to pay 38.5% of all gross licensing revenues received during the
extension period to the Note holders, as payment against the accrued interest
and principal due on the Notes. In the event of default by the Company on the
Notes, the interest rate will increase to 18% per annum, the Note holders will
have the right to appoint a majority of the Board of Directors of the Company
and the Company's assets will be subject to foreclosure.

3.  Earnings (Loss) Per Common Share

Net income (loss) per common share is computed using the Financial Accounting
Standards Board's Statement of Financial Accounting Standards (SFAS) No. 128,
"Earnings Per Share" (EPS).


                                       6
<PAGE>   7

Basic income or loss per common share is computed by dividing the net income or
loss by the weighted-average number of common shares outstanding during the
period.

Diluted income or loss per share is computed using the treasury stock method,
based upon the weighted-average number of common shares, dilutive common stock
equivalent shares and the assumed conversion of any dilutive convertible
securities outstanding during the period.

4.       Recently Issued Accounting Standards

In June 1997, the FASB issued SFAS No. 131, "Disclosures about Segments of an
Enterprise and Related Information." SFAS No. 131, which is effective for fiscal
years beginning after March 15, 1997, establishes new disclosure requirements
for operating segments, including products, services, geographic areas, and
major customers. The Company has adopted SFAS No. 131 for the 1999 fiscal year,
but does not expect the new accounting standard to have a material effect on the
Company's reported financial results.

5.       Subsequent Events

Xenometrix completed a restructuring February 1, 1999, resulting in a reduction
of the Company's work force to four full time employees. Stephen J. Sullivan,
President and Chief Executive Officer resigned and will remain on the Board of
Directors as non-executive Chairman. Pauline Gee has been elected President and
Chief Scientific Officer. A substantial portion of the Company's occupied
premises was subleased to a biotechnology company effective November 1, 1998.
Management believes these changes will reduce future overhead significantly
while still allowing for the full production of its line of gene profiling and
mutagenicity kits, services of its Client Research Laboratory and future
sublicensing arrangements. The Company has resumed shipping of mammalian gene
profiling kits.

Subsequent to this restructuring, the Company has granted two non-exclusive
licenses for its gene expression profiling patents, bringing the total to
fifteen licenses in this field. In addition, the Company granted its first
non-exclusive license for the Company's proprietary automated Ames technology in
this quarter. These licenses incorporate up-front fees and potential future
revenues as well as potential future business and research collaborations.



                                       7
<PAGE>   8




ITEM 2.                          XENOMETRIX, INC.
                     MANAGEMENT'S DISCUSSION AND ANALYSIS OF
                  FINANCIAL CONDITION AND RESULTS OF OPERATIONS

     The following discussion of the results of operations and financial
condition should be read in conjunction with the financial statements and notes
thereto appearing elsewhere in this Report. Except for the historical
information contained herein, this Report contains forward-looking statements
that involve risks and uncertainties. Xenometrix's actual results could differ
materially from those discussed in this Report. Factors that could cause or
contribute to such differences include, but are not limited to, those discussed
in this Report and any documents incorporated herein by reference, as well as in
the Xenometrix Annual Report on Form 10-KSB for the fiscal year ended June 30,
1998.

OVERVIEW

     The Company continues to offer non-exclusive licenses of its intellectual
property. On January 22, 1998, the Company was granted a broad basic patent by
the European Patent Office covering most gene expression profiles resulting from
the exposure of eukaryotic cells (including human, animal and yeast cells) to
pharmaceutical compounds and other chemical entities. On September 22, 1998, the
United States Patent and Trademark Office issued a patent to the Company
covering similar claims in the United States. The Company's strategy to offer
non-exclusive licenses has resulted in sixteen agreements to date. The Company
continues to pursue broad business collaborations with parties whose current or
future business activities may be complementary to those of the Company.

     The Company serves the drug safety and chemical markets, and has been
focusing a significant portion of its effort and resources developing and
marketing its products and services to pharmaceutical companies for testing,
evaluation and optimization of their lead compounds. The timing and amount of
revenues from sales of products and services to the drug discovery and
development market and chemical markets cannot be predicted with certainty.
Similarly, the Company's ability to enter into license agreements and meaningful
collaborative arrangements with customers or other potential collaborators and
licensees cannot be predicted with a high degree of accuracy. Accordingly,
results of operations for any period may be unrelated to results of operations
for any other period and are likely to fluctuate sharply. In addition,
historical results should not be viewed as indicative of future operating
results.

     As of May 14, 1999 the Company has cash of approximately $197,000. The
Company estimates that its current resources together with projected collections
on accounts receivable from customers will be sufficient to meet its operating
needs through approximately August, 1999. Xenometrix is currently in discussions
with several companies regarding licensing of the Company's U. S. and European
gene profiling patents, and is hopeful that additional revenue from these
licenses will be sufficient to fund the Company's operating needs for the next
several months. The Company subleased a portion of its facilities to another
company, which

                                       8
<PAGE>   9

enabled the Company to retain its modern, state-of-the-art facility while
reducing its monthly expenditures.

     The Company also has approximately $284,000 debt remaining from $1,500,000
of the Notes that are due June 15, 1999, subject to further extension. The
Company believes that it can obtain a further extension of the due date of the
Notes because a substantial portion of the licensing revenue generated will go
towards paying down the principal. However, the continued presence of the debt
and the periodic need to obtain additional extensions on the maturity date of
the bridge note has fueled uncertainty over the Company's prospects for
survival. This uncertainty has been a potential obstacle to continued licensing
as well as to developing strategic partners. The actions taken in recent months
are designed to strengthen the Company's prospects for successful operation and
has reduced concerns over the Company's survival.

RESULTS OF OPERATIONS

COMPARISON OF QUARTERS ENDED MARCH, 1999 AND 1998

     Revenue. For the quarter ended March 31, 1999, revenue increased to
approximately $2,019,000 from $103,000 reported in the comparable quarter of the
prior year. The increase was attributable to revenue from up-front licensing
fees relating to the Company's issued patents in the United States and Europe.
Sales of products and service revenue from the Company's Client Research
Laboratory decreased slightly to $97,000 from $103,000 reported in the prior
year.

     Gross Profit. For the quarter ended March 31, 1999, gross profit increased
to $1,679,000 from a loss of $11,000 reported in the prior year. The increase in
gross profit was due to licensing fees where there was no licensing activities
in the comparable quarter of the prior year. The cost of licensing revenue of
approximately $237,000 represents royalties paid to the Universities of Harvard
and California, Berkeley under the Company's existing licensing agreements and a
portion of the amortization of the costs associated with the patents and legal
expenses in prosecuting the patents. Gross profit margins on revenue from sales
of products and services were approximately -9%. This negative gross profit
margin is connected with the restructuring initiated February, 1999.

     Research and Development Expenses (R&D). R&D expenses for the quarter ended
March 31, 1999, decreased 77% to $54,000 from $234,000 reported in the same
quarter of the prior year. This decrease was primarily attributable to reduced
headcount in the R&D department and personnel costs in the R&D department being
allocated to the cost of products and services sold. Laboratory supplies and
most other expenses in the R&D department were also down in the current quarter,
compared to the comparable quarter of the prior year.

     Selling, General and Administrative Expenses (SG&A). For the quarter ended
March 31, 1999, SG&A expenses were $187,000, down 60% from $484,000 in the prior
year. This decrease was primarily attributable to lower business development,
legal, finance, accounting 


                                       9
<PAGE>   10

and administrative costs resulting from personnel reductions in February 1999
and lower Board of Directors costs associated with reducing the size of the
Board and replacing cash compensation to Board members with increased stock
option grants.

     Interest Expense, Net. During the quarter ended March 31, 1999, the Company
incurred net interest expense of $35,000 compared to $290,000 in the comparable
quarter of the prior fiscal year. The net interest expense incurred included
interest accrued on the Notes at the stated interest rate and the amortization
of the values attributable to the warrants issued in conjunction with the Notes.
The interest rate on the Notes remains at 12% per annum and Xenometrix will
continue to pay 38.5% of gross licensing revenues received during the extension
period to the Note holders as payment against the outstanding interest and
principal due on the Notes. The net interest expense decreased approximately 90%
from the comparable quarter in the prior year because the Notes have been
substantially repaid. In the event of a sale of the Company prior to June 15,
1999, the Notes will be due at the closing of such sale.

     Net Income (Loss). For the quarter ended March 31, 1999, there was a net
income of $1,403,000 or $0.48 per share compared to a loss of $1,019,000 or
$0.35 per share, reported for the third quarter of fiscal year, 1998. The
earnings would have been $0.44 per diluted share.

IMPACT OF YEAR 2000 ISSUES

     The Year 2000 issue is related to computer software utilizing two digits
rather than four to define the appropriate year. As a result, any of the
Company's computer programs or any of the Company's suppliers or vendors that
have date sensitive software may incur system failures or generate incorrect
data if "00" is recognized as 1900 rather than 2000.

     The Company has evaluated the proprietary software used to facilitate
performing, analyzing and interpreting the results of its assays, and the
proprietary software used in conjunction with its bioinformatics data base, and
found them to appropriately address the date issues associated with the year
2000. The Company believes that all dates in its proprietary software are stored
with either a minimum of four digits for the year or as a text string, thereby
preventing inappropriate sequencing of date sensitive information. While the
Company believes that its proprietary software will not produce any material
problems, erroneous calculations or degradation of performance as a result of
Year 2000 issues, users are advised that the Company's software must be run on
Year 2000 compliant platforms.

     The Company plans to verify whether its major suppliers, service providers
and financial institutions are Year 2000 compliant, however there can be no
assurance that the systems and networks of its key suppliers and customers will
not be affected by Year 2000 issues, which could have an adverse effect on the
Company's business, operating results and financial condition. The Company
believes, based upon the evaluations performed upon its proprietary software and
the claims of Year 2000 compliance made by the providers of non-proprietary
software used by the Company, that the impact of Year 2000 will not be material.
However,


                                       10
<PAGE>   11

to the extent the Company or third parties upon which it relies do not timely
achieve Year 2000 readiness, the Company's results of operations may be
adversely affected.

LIQUIDITY AND CAPITAL RESOURCES

     At March 31, 1999, the Company had cash of $85,000. During the three month
period ended March 31, 1999, $1,139,000 was provided by the Company's activities
and $179,000 was invested in patents. There were no cash resources generated
from financing activities, and $1,216,000 was used in repayment of a substantial
portion of senior promissory Notes.

     As of May 14, 1999, the Company had cash of approximately $197,000 compared
to $85,000 at the end of March 31, 1999. The Company has signed an additional
licensing agreement since the end of the last quarter in addition to the nine
non-exclusive agreements executed in the March 31, 1999 quarter. The Company is
currently in discussions with several companies regarding licensing of the
Company's intellectual property, and is hopeful that additional revenue from
these licenses will be sufficient to fund the Company's operating needs for the
next several months.

     The Company believes that it is unlikely that it can generate sufficient
licensing revenue and revenue from products and services to fund the Company's
operations and pay off the remaining balance of the Notes on the maturity date.
The Company believes that it can obtain a further extension of the due date of
the Notes because a substantial portion of the licensing revenue generated will
go towards paying down the remaining principal. However, it is exploring
strategic partnerships, including but not limited to, the sale of the Company.




                                       11
<PAGE>   12



                           PART II--OTHER INFORMATION


ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K.


(a)  Exhibits

         27.1      Summary Financial Information Schedule



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





                                       12
<PAGE>   13



                                   SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Company
has duly caused this Report to be signed on its behalf.

                                     XENOMETRIX, INC.



                                     /s/ Pauline Gee

May 14, 1999                         Pauline Gee
                                     President, Chief Scientific Officer







                                       13
<PAGE>   14



                                  EXHIBIT INDEX


Exhibit No.                         Description
-----------                         -----------


27.1              Summary Financial Information Schedule

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




                                       14