<PAGE>

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM 10-Q

[X] QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
EXCHANGE ACT OF 1934 For the period ended March 31, 2000.

                                                        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: 000-20931

                          VENTANA MEDICAL SYSTEMS, INC.
             (Exact name of registrant as specified in its charter)

                 Delaware                                94-2976937
     (State or other jurisdiction of                  (I.R.S. employer
     incorporation or organization)                  identification no.)

           3865 North Business                             85705
              Center Drive                               (Zip Code)
               Tucson, AZ
 (Address of principal executive offices)

       Registrant's telephone number, including area code: (520) 887-2155

                                 Not Applicable
              (Formal name, former address and former fiscal year,
                          if changed from last report)

         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 [ ]


                Applicable Only to Issuers Involved in Bankruptcy
              (Formal name, former address and former fiscal year,
                          if changed from last report)

         Indicate by check mark whether the registrant has filed all documents
and reports required to be filed by Sections 12, 13, or 15(d) of the Securities
Exchange Act of 1934 subsequent to the distribution of securities under a plan
confirmed by the court.    Yes [X]   No [ ]


                      Applicable Only to Corporate Issuers

         Indicate the number of shares outstanding of each of the issuer's
classes of common stock, as of the latest practical date.
Common Stock, $0.001 par value --- 15,085,892 shares as of April 28, 2000.

<PAGE>

                          VENTANA MEDICAL SYSTEMS, INC.


                               INDEX TO FORM 10-Q
                               ------------------


Part I.  Financial Information

    Item 1.  Financial Statements

             Condensed Consolidated Balance Sheets
             March 31, 2000 (Unaudited) and December 31, 1999................ 3

             Condensed Consolidated Statements of Operations
             Three months ended March 31, 2000 and 1999 (Unaudited).......... 4

             Condensed Consolidated Statements of Cash Flows
             Three months ended March 31, 2000 and 1999 (Unaudited).......... 5

             Notes to Condensed Consolidated Financial Statements............ 6

    Item 2.  Management's Discussion and Analysis of Financial Condition
             and Results of Operations.......................................10

Part II. Other Information

    Item 1.  Legal Proceedings...............................................12

    Item 2.  Changes in Securities and Use of Proceeds.......................13

    Item 6.  Exhibits and Reports on Form 8-K................................13

                                    Signature................................14

                                       2
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                          VENTANA MEDICAL SYSTEMS, INC.
                     CONDENSED CONSOLIDATED BALANCE SHEETS
                        (in thousands except share data)


                                                        March 31,   December 31,
                                                          2000         1999
                                                      ------------  ------------
                                                       (Unaudited)    (Note)
                          ASSETS
Current assets:
   Cash and cash equivalents                          $    46,569   $     1,787
   Accounts receivable                                     21,147        20,776
   Inventories (Note 2)                                    14,072        13,474
   Prepaid Expenses                                           802           574
   Deferred tax benefit, current portion                    1,434         1,692
   Other current assets                                       439           722
                                                      ------------  ------------
Total current assets                                       84,463        39,025
Property and equipment, net                                14,346        14,441
Intangibles, net                                           15,148        14,178
Other assets                                                2,688         1,084
Deferred tax benefit, long term portion                     4,433         4,433
                                                      ------------  ------------
Total assets                                          $   121,078   $    73,161
                                                      ============  ============

LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
   Accounts payable                                   $     2,782   $     4,017
   Other current liabilities                                5,660         6,600
                                                      ------------  ------------
Total current liabilities                                   8,442        10,617
Long term debt                                              1,823         2,044
Stockholders' equity
   Common stock - $.001 par value; 50,000,000 shares
     authorized; 15,060,017 and 13,593,640 shares
     issued and outstanding at March 31, 2000 and
     December 31, 1999, respectively                           15            14
   Additional Paid-In Capital                             129,855        80,542
   Accumulated deficit                                    (18,372)      (19,341)
   Cumulative other comprehensive income                      (85)         (115)
   Treasury Stock - 40,000 shares, at cost                   (600)         (600)
                                                      ------------  ------------
Total stockholders' equity                                110,813        60,500
                                                      ------------  ------------
Total liabilities and stockholders' equity            $   121,078   $    73,161
                                                      ============  ============


  Note:  The consolidated balance sheet at December 31, 1999 has been derived
         from the audited financial statements at that date but does not include
         all of the information and footnotes required by generally accepted
         accounting principles for complete financial statements.

  See accompanying notes

                                       3
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                          VENTANA MEDICAL SYSTEMS, INC.
                 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                      (in thousands except per share data)
                                   (Unaudited)


                                                         Three Months Ended
                                                              March 31,
                                                              ---------
                                                          2000         1999
                                                      ------------  ------------
Sales:
  Instruments                                         $     5,828   $     5,120
  Reagents and other                                       12,001        10,512
                                                      ------------  ------------
    Total net sales                                        17,829        15,632
Cost of goods sold                                          6,134         4,988
                                                      ------------  ------------
Gross profit                                               11,695        10,644
Operating expenses:
  Research and development                                  1,984         1,629
  Selling, general and administrative                       7,960         7,399
  Amortization of intangibles                                 278           253
                                                      ------------  ------------
Income from operations                                      1,473         1,363
Other income (expense)                                        (48)           24
                                                      ------------  ------------
Income before income taxes                                  1,425         1,387
Provision for income tax (Note 5)                             456           138
                                                      ------------  ------------
Net income                                            $       969   $     1,249
                                                      ============  ============
Net income per share (Note 3)
  Basic                                               $      0.07   $      0.09
                                                      ============  ============
  Diluted                                             $      0.06   $      0.09
                                                      ============  ============

  See accompanying notes

                                       4
<PAGE>

                          VENTANA MEDICAL SYSTEMS, INC.
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                 (in thousands)
                                   (Unaudited)


                                                         Three Months Ended
                                                              March 31,
                                                              ---------
                                                          2000         1999
                                                      ------------  ------------
OPERATING ACTIVITIES:
Net Income                                            $       969   $     1,249
Adjustments to reconcile net income to net cash
  provided by (used in) operating activities:
    Change in deferred tax benefit, net                       258             -
    Depreciation and amortization                           1,286           893
    Changes in operating assets and liabilities, net       (4,545)           61
                                                      ------------  ------------
Net cash (used in) provided by operating activities        (2,032)        2,203

INVESTING ACTIVITIES:
Purchase of property and equipment, net                    (1,024)       (2,885)
Purchase of intangible assets                              (1,250)          (45)
                                                      ------------  ------------
Net cash used in investing activities                      (2,274)       (2,930)

FINANCING ACTIVITIES:
Repayment of debt - net                                      (256)          (64)
Issuance of stock - net                                    49,314           480
                                                      ------------  ------------
Net cash provided by financing activities                  49,058           416

Effect of exchange rate change on cash                         30             -
                                                      ------------  ------------

Net increae (decrease) in cash and cash equivalents        44,782          (311)

Cash and cash equivalents, beginning of period              1,787         2,424
                                                      ------------  ------------
Cash and cash equivalents, end of period              $    46,569   $     2,113
                                                      ============  ============

See accompanying notes

                                       5
<PAGE>

                          VENTANA MEDICAL SYSTEMS, INC.

              Notes to Condensed Consolidated Financial Statements
                                   (Unaudited)


1.   SIGNIFICANT ACCOUNTING POLICIES

The accompanying condensed consolidated financial statements are unaudited. They
have been prepared by the Company pursuant to the rules and regulations of the
Securities and Exchange Commission and are subject to year-end audit by
independent auditors. Certain information and footnote disclosure normally
included in financial statements prepared in accordance with generally accepted
accounting principles have been condensed or omitted pursuant to such rules and
regulations. It is suggested that the condensed consolidated financial
statements be read in conjunction with the financial statements and notes
included in the Company's Annual Report and Form 10-K for the year ended
December 31, 1999.

The information furnished reflects all adjustments which, in the opinion of
management, are necessary for a fair presentation of results for the interim
periods. Such adjustments consisted only of normal recurring items. It should
also be noted that results for the interim periods are not necessarily
indicative of the results expected for the full year or any future period.

The presentation of these consolidated financial statements in conformity with
generally accepted accounting principles requires management to make estimates
and assumptions that affect the reported amounts of assets and liabilities and
disclosures of contingent assets and liabilities at the date of the financial
statements and the reported amounts of revenues and expenses during the
reporting period. Actual results could differ from those estimates.


2.   INVENTORIES

Inventories consist of the following:

                                                   March 31,   December 31,
                                                     2000         1999
                                                 ------------  ------------
                                                      (in thousands)

              Raw material and work-in-process   $     6,879   $     5,729
              Finished goods                           7,193         7,745
                                                 ------------  ------------
                                                 $    14,072   $    13,474
                                                 ============  ============

                                       6
<PAGE>

                          VENTANA MEDICAL SYSTEMS, INC.

              Notes to Condensed Consolidated Financial Statements
                                   (Unaudited)


3.   EARNINGS PER SHARE

The following sets forth the computation of basic and diluted earnings per share
for the periods indicated (in thousands except per share data).


                                                         Three Months Ended
                                                              March 31,
                                                              ---------
                                                          2000         1999
                                                      ------------  ------------

         Net income                                   $       969   $     1,249
         Weighted average common shares
           outstanding, basic                              14,305        13,404
         Add: dilutive stock options and warrants           2,162         1,174
                                                      ------------  ------------
         Weighted average common shares
           outstanding, diluted                            16,467        14,578
                                                      ============  ============
         Net income per share, basic                  $      0.07   $      0.09
                                                      ============  ============
         Net income per share, diluted                $      0.06   $      0.09
                                                      ============  ============

                                       7
<PAGE>

                          VENTANA MEDICAL SYSTEMS, INC.

              Notes to Condensed Consolidated Financial Statements
                                   (Unaudited)


4.   COMPREHENSIVE INCOME

The components of comprehensive income for the three month periods ended March
31, 2000 and 1999 are as follows (in thousands):

                                                         Three Months Ended
                                                              March 31,
                                                              ---------
                                                          2000         1999
                                                      ------------  ------------

         Net income                                   $       969   $     1,249

         Foreign currency translation                          30             -
                                                      ------------  ------------
         Comprehensive income                         $       999   $     1,249
                                                      ============  ============

Accumulated other comprehensive income consists exclusively of foreign currency
translation adjustments.


5.   PROVISION FOR INCOME TAXES

The 2000 provision for income taxes reflects the estimated annual effective tax
rate. The effective tax rate is less than the U.S. statutory rate due to
utilization of net operating loss carryforwards by the Company's subsidiary in
France. Prior to 2000, the Company's effective tax rate was zero due to
reduction of deferred tax asset valuation allowances. The tax provision recorded
in the first quarter of 1999 was subsequently reversed.


6.   LINE OF CREDIT

The Company had up to $10,000 available under a line of credit arrangement with
a bank which is subject to renewal on March 31, 2001. Borrowings under the line
are collateralized by the Company's receivables, inventories, machinery and
equipment, and intellectual property. Borrowings under the line are limited
based on outstanding accounts receivable, which as of March 31, 2000, resulted
in available borrowing of $7.3 million. The line contains certain financial
covenants (measured quarterly) with which the Company must comply which, among
other things, prohibits the payment of dividends on the Company's stock and
limits the number of treasury shares the Company may purchase. The line of
credit arrangement also provides for quarterly payment of unused line commitment
fees. No amounts were outstanding under this agreement at March 31, 2000 or
1999.

                                       8
<PAGE>

7.   OPERATING SEGMENT AND ENTERPRISE DATA

The Company has two reportable segments: North America (the United States and
Canada) and International (primarily France, Germany, and Japan). Segment
information at and for the three months ended March 31, 2000 and 1999 follows
(in thousands):

<TABLE>
<CAPTION>

                                                Three months ended March 31, 2000
                                      ----------------------------------------------------
                                         North                      Elimina-
                                        America    International     tions        Totals
                                      ----------------------------------------------------
  <S>                                 <C>           <C>           <C>           <C>
  Sales to external customers         $  13,418     $   4,411     $       -     $  17,829
  Segment profit (loss)                     559           410                         969
  Segment assets                        122,863        15,328       (17,113)      121,078
</TABLE>


<TABLE>
<CAPTION>
                                                Three months ended March 31, 1999
                                      ----------------------------------------------------
                                         North                      Elimina-
                                        America    International     tions        Totals
                                      ----------------------------------------------------
  <S>                                 <C>           <C>           <C>           <C>
  Sales to external customers         $  12,740     $   2,892     $       -     $  15,632
  Segment profit (loss)                   1,413          (205)           41         1,249
  Segment assets                         70,966         8,824       (21,649)       58,141
</TABLE>



                                       9
<PAGE>

ITEM 2.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITIONS AND
         RESULTS OF OPERATIONS

The following discussion of the financial condition and results of operations of
Ventana Medical Systems, Inc. ("Ventana" or "the Company") should be read in
conjunction with the Condensed Consolidated Financial Statements and related
Notes thereto included elsewhere in this Form 10-Q. This Report on Form 10-Q
contains certain forward-looking statements within the meaning of Section 27A of
the Securities Act of 1933 and Section 21E of the Securities Exchange Act of
1934. Actual events or results may differ materially from those anticipated by
such forward-looking statements as a result of the factors described herein and
in the documents incorporated herein by reference.


OVERVIEW

Ventana develops, manufactures and markets proprietary instrument/reagent
systems that automate tissue preparation, immunohistochemistry ("IHC") tests,
special stains ("SS") tests and IN SITU hybridization ("ISH") tests for the
analysis of cells and tissues on microscope slides.


RESULTS OF OPERATIONS

NET SALES

Net sales for the three months ended March 31, 2000 as compared to the same
period in 1999 increased 14% to $17.8 million from $15.6 million. The increase
in net sales was attributable to 14% increases in both instrument and reagent
sales. Instrument sales increased primarily due to strong international growth
in all instrument types. Reagent revenue continued a strong growth trend due to
a growing installed base, while service revenue also increased due to the
growing number of instruments coming off warranty. Sales increased in the first
three months of 2000 compared to the same period in 1999 in both geographic
segments: 5% in the U.S. ($13.4 million versus $12.7 million), and 53%
internationally ($4.4 million versus $2.9 million). Sales force realignment and
training programs negatively impacted U.S. revenues in the first quarter of
2000, but are expected to result in more rapid revenue growth for the balance of
the year.

GROSS PROFIT

Gross profit for the three months ended March 31, 2000 increased to $11.7
million from $10.6 million for the same period in 1999. The Company's gross
margin for the three month period decreased to 66% from 68% in the same period
of the prior year. The decline in gross margin percentage was due primarily to
lower instrument production resulting in unfavorable manufacturing cost
absorption in comparison to the first quarter of 1999.

                                       10
<PAGE>

RESEARCH AND DEVELOPMENT

Research and development expenses were $2.0 million for the three months ended
March 31, 2000, a 22% increase over the prior year. The increase results
primarily from substantial development work on new products.

SELLING, GENERAL AND ADMINISTRATIVE ("SG&A")

Presented below is a summary of SG&A expense for the three months ended March
31, 2000 and 1999 (dollars in thousands).


                                    Three Months Ended
                                         March 31,
                                         ---------
                                     2000         1999
                                 ------------  ------------
                                          %             %
                                        Sales         Sales
                                 ------------  ------------
Sales and marketing              $6,368   36%  $6,067   39%
Administration                    1,592    9%   1,332    8%
                                 ------------  ------------
Total SG&A                       $7,960   45%  $7,399   47%
                                 ============  ============

SG&A expense for the three months ended March 31, 2000 increased to $8.0 million
from $7.4 million for the same period of the prior year. Total SG&A expenses
increased in absolute terms due primarily to the Company's expanding
international business base plus costs associated with implementing new
administrative systems and functions. As a percentage of net sales, however,
SG&A expenses decreased due to leveraging of the sales and marketing
organization as it approaches full staffing levels.

AMORTIZATION OF INTANGIBLES

Intangible assets consist primarily of goodwill, customer base and developed
technology resulting from acquisitions and patents. Such assets are amortized
over estimated useful lives of 5 to 20 years resulting in quarterly costs
approximating $0.3 million. Additionally, the Company will review the utility of
these assets each quarter to assess their continued value and recognize any
impairment should the Company determine such a condition exists.

LIQUIDITY AND CAPITAL RESOURCES

As of March 31, 2000, the Company's principal source of liquidity consisted of
cash and cash equivalents of $46.6 million. See Part II, Item 2 "Changes in
Securities and Use of Proceeds". The Company also had an unused $10 million
revolving bank credit facility. Any borrowings under the Company's bank credit
facility are secured by a pledge of substantially all of the Company's assets
and bear interest at the bank's prime rate.

The Company has used a portion of its available resources during the current
year for fixed asset expenditures and development of software for future new
products. In addition, resources were used for a license and development
agreement with AccuMed, Inc. and the acquisition of the assets of Quantitative

                                       11
<PAGE>

Diagnostics Laboratories, Inc. (QDL). The Company anticipates that its remaining
capital resources will be used for working capital and general corporate
purposes. Pending such uses, the Company intends to invest its cash resources in
short-term, interest-bearing, investment grade securities.

During the three months ended March 31, 2000, net cash used in operations and
investing activities increased to $4.3 million, versus $0.7 million in the three
months ended March 31, 1999. The increase was primarily due to the AccuMed and
QDL transactions, as well as greater working capital needs due to growth in the
Company's base business.

The Company has entered into a contract for construction of a new corporate
headquarters and manufacturing facility in suburban Tucson, Arizona. The site of
the new facility is approximately 15 miles from the current headquarters and
will consolidate operations that are presently located in several leased
facilities around Tucson. Construction is expected to begin in the third quarter
of 2000, with occupancy beginning in mid-2001. Funding for the new facility is
anticipated to be obtained from existing cash resources.

The Company believes that its existing capital resources, together with cash
generated from product sales and available borrowing capacity under its bank
credit facilities will be sufficient to satisfy its working capital requirements
for the near future.


PART II - OTHER INFORMATION

ITEM 1.   LEGAL PROCEEDINGS.

In January 1997, four individuals who are former BioTek noteholders who held in
the aggregate approximately $1.1 million in principal amount of BioTek notes
filed an action, Tse, et al v. Ventana Medical Systems, Inc., et al. No. 97-37
("Tse Action"), against us and certain of our then current directors and
stockholders in the United States District Court for the District of Delaware.
The complaint alleges, among other things, that we violated federal and
California securities laws and engaged in common law fraud in connection with
the BioTek shareholders' consent to the February 1996 merger of BioTek into
Ventana and the related conversion of BioTek notes into Ventana notes, which
were subsequently repaid. Plaintiffs seek substantial compensatory damages
several times in excess of the principal amount of their BioTek notes, as well
as substantial punitive damages, and fees and costs. On April 25, 1997,
plaintiffs filed an Amended Complaint. The Amended Complaint makes the same
allegations as the original Complaint, and adds a claim under North Carolina
securities laws. In May of 1997, we made a motion to transfer the action to the
district of Arizona, or alternately to the Central District of California, which
was denied by the court. On December 16, 1997, we filed a motion to dismiss the
Amended Complaint. This motion was partially accepted and partially denied by
the Court. On March 8, 1999, plaintiffs filed a Second Amended Complaint. The
Second Amended Complaint makes the same allegations as the original and Amended
Complaints, deletes the claim made under North Carolina securities laws and the
claim made under California Blue Sky laws, and adds stockholders as defendants.
Based on the facts known to date, we believe that the claims are without merit
and we intend to vigorously contest this suit. After consideration of the nature
of the claims and the facts relating to the merger and the BioTek note exchange,
we believe we have meritorious defenses to the claims and that resolution of
this matter will not have a material adverse effect on our business, financial
condition and results of operations; however, the results of the proceedings are
uncertain and there can be no assurance to that effect.

                                       12
<PAGE>

In April 1999, a former BioTek noteholder filed an action, Leung, et al. v. Jack
W. Schuler, et al., No. 17089, against us and certain of our then current
directors and stockholders in the Delaware State Chancery Court, New Castle
County. The complaint, brought individually and on behalf of a purported class,
makes virtually the same allegations made in the Tse Action and seeks recovery
under breach of contract and breach of fiduciary duty theories. On May 6, 1999
we filed a motion to dismiss the complaint. On February 29, 2000, the court
issued a memorandum opinion granting our motion and dismissing the complaint in
its entirety.

On June 15, 1999 we filed a proof of claim against Oncor, Inc. in an action
pending in the United States Bankruptcy Court for the District of Delaware
titled In re Oncor, Inc., No. 9-437 (JJF). Our claims arise out of an Asset
Purchase Agreement dated November 23, 1998 and related documents wherein we
acquired Oncor's unincorporated In Situ Hybridization Technology Division and
rights related thereto. In February 2000, we filed an amended proof of claim
alleging, inter alia, that Oncor breached the terms of the Asset Purchase
Agreement by purporting to transfer or assign to us Oncor's rights under a
license agreement, which were not transferable or assignable under the
circumstances then existing. The amended proof of claim seeks damages of no less
than approximately $7.3 million. We believe our claims are meritorious and that
we will prevail, however, the results of the proceedings are uncertain and there
can be no assurance to that effect.

On December 9, 1999 we filed an action, Ventana Medical Systems, Inc. v.
Cytologix Corp., No. CIV99-606 TUC FRZ, alleging patent infringement seeking
monetary damages and injunctive relief in the United States District Court in
Tucson. The original complaint was amended March 21, 2000 by the addition of
another patent to the litigation. We believe our claims are meritorious and that
we will prevail, however, because the action is relatively new, results of the
proceedings are uncertain and there can be no assurance to that effect.

In February 2000, we settled the lawsuit in the Northern District of California
filed by a former employee.


ITEM 2.  CHANGES IN SECURITIES AND USE OF PROCEEDS

On March 30, 2000, we completed a private placement of 1,250,000 shares of our
Common Stock at a price of $40 per share, for total gross proceeds of $50
million, to institutional investors pursuant to the exemption from registration
provided by Section 4(2) and Regulation D of the Securities Act. We received all
proceeds of the offering less a commission of 5.5% to Bear Stearns & Co. Inc. as
placement agent, for a total of $2,750,000. We have an effective registration
statement on file with the Commission covering the shares sold in this
placement.


ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K

         (a)  Exhibits

              27.1     Financial Data Schedule.

         (b)  Reports on Form 8-K.

              No reports were filed on Form 8-K during the quarter
ended March 31, 2000.

                                       13
<PAGE>

                                    SIGNATURE


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

                                              Ventana Medical Systems, Inc.



Date: May 15, 2000                         By:  /S/ Jay Meridew
                                              ----------------------------------
                                              Jay Meridew
                                              Vice President of Finance

                                       14