<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 QUARTERLY PERIOD ENDED MARCH 31, 1999

                                       OR

       [   ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF
                         THE SECURITIES EXCHANGE ACT OF 1934

                           COMMISSION FILE NO. 0-23659

                                   VYSIS, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

       DELAWARE                                        36-3803405
(STATE OR OTHER JURISDICTION OF         (I.R.S. EMPLOYER IDENTIFICATION NUMBER)
INCORPORATION OR ORGANIZATION)


         3100 WOODCREEK DRIVE                             60515-5400
         DOWNERS GROVE, ILLINOIS                          (ZIP CODE)
 (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)

      REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE: (630) 271-7000

         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   ___  

     Number of shares of Common Stock, par value $.001 per share, outstanding as
of May 17, 1999: 9,808,157
<PAGE>

                                   VYSIS, INC.

                                    FORM 10-Q

                  FOR THE QUARTERLY PERIOD ENDED MARCH 31, 1999

                                TABLE OF CONTENTS
<TABLE>
<CAPTION>
                                                                                          PAGE
                                                                                          ----
<S>                                                                                     <C>
                          PART I: FINANCIAL INFORMATION

ITEM 1:        Financial Statements

                    Consolidated Balance Sheets
                       As of March 31, 1999 and December 31, 1998 ........................   2

                    Consolidated Statements of Operations                                 
                       For the three months ended March 31, 1999 and 1998 ................   3

                    Consolidated Statements of Comprehensive Operations                   
                       For the three months ended March 31, 1999 and 1998 ................   4

                    Consolidated Statements of Cash Flows                                 
                       For the three months ended March 31, 1999 and 1998 ................   5

                    Notes to Consolidated Financial Statements ...........................   6
                                                                                          
ITEM 2:        Management's Discussion and Analysis of Financial Condition                
                    and Results of Operations ............................................  10
                                                                                          
ITEM 3:        Quantitative and Qualitative Disclosure About Market Risk .................  15
                                                                                          
                           PART II: OTHER INFORMATION                                     

ITEM 1:        Legal Proceedings .........................................................  16

ITEM 2:        Changes in Securities and Use of Proceeds .................................  17

ITEM 6:        Exhibits and Reports on Form 8-K ..........................................  17

SIGNATURE ................................................................................  18
</TABLE>

                                    1

<PAGE>


                          PART I. FINANCIAL INFORMATION
                          ITEM 1. FINANCIAL STATEMENTS

                                   VYSIS, INC.
                   (AN INDIRECT SUBSIDIARY OF BP AMOCO P.L.C.)

                           CONSOLIDATED BALANCE SHEETS

               (IN THOUSANDS, EXCEPT SHARE AND PER SHARE AMOUNTS)
                                   (UNAUDITED)
<TABLE>
<CAPTION>
                                                                                          MARCH 31,       DECEMBER 31,
                                                                                            1999              1998
                                                                                        -------------     ------------
<S>                                                                                     <C>               <C>
ASSETS
Current assets:
     Cash and cash equivalents ......................................................        $  2,658         $  4,672
     Short-term investments .........................................................          10,950           13,667
     Accounts receivable, net .......................................................           4,975            6,106
     Current portion of long-term lease receivables ................................              429              378
     Inventories ....................................................................           2,623            2,487
     Other current assets ...........................................................           1,300              782
                                                                                             --------         --------
         Total current assets .......................................................          22,935           28,092
Property and equipment, net .........................................................           3,627            3,879
Investment ..........................................................................             ---              562
Long-term lease receivables .........................................................             469              626
Other assets ........................................................................           1,816            1,884
                                                                                             --------         --------
         Total assets ...............................................................        $ 28,847         $ 35,043
                                                                                             --------         --------
                                                                                             --------         --------
LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
     Current portion of long-term debt ..............................................        $    517         $    553
     Accounts payable and accrued liabilities .......................................           7,758            9,475
     Deferred revenue ...............................................................             908              966
                                                                                             --------         --------
         Total current liabilities ..................................................           9,183           10,994
                                                                                             --------         --------

Long-term debt ......................................................................             352              523
                                                                                             --------         --------
                                                                                             --------         --------
Contingency (Note 9)

Stockholders' equity:
     Convertible Preferred Stock, $0.001 par value; 10,000,000 shares
         authorized: Series A; 6,200,000 shares designated; none issued and
         outstanding at March 31, 1999 and December 31, 1998 .......................              ---              ---
         Series B; 553,126 shares designated; none issued and outstanding
         at March 31, 1999 and December 31, 1998 ...................................              ---              ---
     Common stock, $0.001 par value; 35,000,000 shares authorized; 9,806,888
         issued and outstanding at March 31, 1999; 9,788,401 issued and outstanding 
         at December 31, 1998 .......................................................              10               10
     Additional paid-in capital .....................................................          71,872           71,862
     Deferred compensation ..........................................................             (62)             (81)
     Unrealized gain on investment ..................................................             ---              462
     Cumulative translation adjustment ..............................................            (384)            (101)
     Accumulated deficit ............................................................         (52,124)         (48,626)
                                                                                             --------         --------
         Total stockholders' equity .................................................          19,312           23,526
                                                                                             --------         --------
         Total liabilities and stockholders' equity .................................        $ 28,847         $ 35,043
                                                                                             --------         --------
                                                                                             --------         --------
</TABLE>
               See notes to the consolidated financial statements.


                                    2

<PAGE>



                                   VYSIS, INC.
                   (AN INDIRECT SUBSIDIARY OF BP AMOCO P.L.C.)

                      CONSOLIDATED STATEMENTS OF OPERATIONS

                    (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                            THREE MONTHS ENDED MARCH 31,
                                                                           ------------------------------
                                                                              1999              1998
                                                                           ----------       -------------
<S>                                                                         <C>             <C>
Revenues:
     Product revenue .................................................        $ 5,283         $ 4,559
     Grant and other revenue .........................................            161             492
                                                                              -------         -------
         Total revenues ..............................................          5,444           5,051
Cost of goods sold ...................................................          2,047           2,061
                                                                              -------         -------
Gross profit .........................................................          3,397           2,990
                                                                              -------         -------
Operating expenses:
     Research and development ........................................          2,477           2,577
     Selling, general and administrative .............................          4,421           5,046
     Restructuring expense ...........................................            541             ---
                                                                              -------         -------
         Total operating expenses ....................................          7,439           7,623
                                                                              -------         -------
Loss from operations .................................................         (4,042)         (4,633)
Interest income ......................................................            220             213
Gain on sale of investment ...........................................            357             ---
Interest expense .....................................................            (33)           (131)
                                                                              -------         -------
Net loss .............................................................        $(3,498)        $(4,551)
                                                                              -------         -------
                                                                              -------         -------
Basic and diluted net loss per share .................................        $ (0.36)        $ (0.79)
                                                                              -------         -------
                                                                              -------         -------

Shares used in computing basic and diluted net loss per share ........          9,792           5,759
</TABLE>

               See notes to the consolidated financial statements.


                                    3

<PAGE>



                                   VYSIS, INC.
                   (AN INDIRECT SUBSIDIARY OF BP AMOCO P.L.C.)

               CONSOLIDATED STATEMENTS OF COMPREHENSIVE OPERATIONS

                                 (IN THOUSANDS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                              THREE MONTHS ENDED MARCH 31,
                                                             ------------------------------
                                                                 1999               1998
                                                             -------------      ----------
<S>                                                         <C>                 <C>
Net loss .................................................        $(3,498)        $(4,551)

Other comprehensive income:
     Cumulative translation adjustment ...................           (283)             (3)
     Unrealized holding gain (loss) on investment ........           (105)             26
     Realized loss on investment .........................           (357)            ---
                                                                  -------         -------
         Total other comprehensive income ................           (745)             23
                                                                  -------         -------
Comprehensive loss .......................................        $(4,243)        $(4,528)
                                                                  -------         -------
                                                                  -------         -------
</TABLE>

               See notes to the consolidated financial statements.


                                    4

<PAGE>



                                   VYSIS, INC.
                   (AN INDIRECT SUBSIDIARY OF BP AMOCO P.L.C.)

                      CONSOLIDATED STATEMENTS OF CASH FLOWS

                                 (IN THOUSANDS)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                                           THREE MONTHS ENDED MARCH 31,
                                                                          -----------------------------
                                                                               1999             1998
                                                                          ------------       ----------
<S>                                                                       <C>                <C>
CASH FLOWS FROM OPERATING ACTIVITIES:

     Net loss ...........................................................     $ (3,498)        $ (4,551)
     Reconciliation of net loss to net cash used in operating activities:
         Depreciation and amortization ..................................          429              443
         Gain on sale of investment .....................................         (357)             ---
         Stock compensation .............................................           19               41
         Changes in assets and liabilities:
              Accounts receivable .......................................          807             (762)
              Inventories ...............................................         (209)            (172)
              Other current assets ......................................         (481)             601
              Lease receivables .........................................           58              ---
              Other assets ..............................................           35             (208)
              Accounts payable and accrued liabilities ..................       (1,623)            (755)
              Deferred revenue ..........................................          (50)            (171)
                                                                              --------         --------
         Net cash used in operating activities ..........................       (4,870)          (5,534)
                                                                              --------         --------

CASH FLOWS FROM INVESTING ACTIVITIES:
     Proceeds from maturities of short-term investments .................        9,850              ---
     Proceeds from sale of investment ...................................          457              ---
     Purchases of short-term investments ................................       (7,133)          (7,806)
     Purchases of property and equipment ................................         (125)            (151)
     Increase in other assets ...........................................          (42)             (20)
                                                                              --------         --------
         Net cash provided by (used in) investing activities ............        3,007           (7,977)
                                                                              --------         --------

CASH FLOWS FROM FINANCING ACTIVITIES:
     Proceeds from issuance of common stock .............................          ---           32,145
     Proceeds from option plan exercises ................................           10              ---
     Increase in note payable--BP Amoco .................................          ---            1,665
     Expenses funded by BP Amoco ........................................          ---              153
     Loan repayment to BP Amoco .........................................          ---           (2,000)
     Principal payments on long-term borrowings .........................         (125)             ---
                                                                              --------         --------
         Net cash provided by (used in) financing activities ............         (115)          31,963
Effect of exchange rate changes on cash .................................          (36)             (25)
                                                                              --------         --------
Net increase (decrease) in cash and cash equivalents ....................       (2,014)          18,427
Cash and cash equivalents at beginning of period ........................        4,672              669
                                                                              --------         --------
Cash and cash equivalents at end of period ..............................     $  2,658         $ 19,096
                                                                              --------         --------
                                                                              --------         --------
</TABLE>

               See notes to the consolidated financial statements.


                                    5

<PAGE>



                                VYSIS, INC.

               NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                               (UNAUDITED)


NOTE 1--ORGANIZATION AND BUSINESS:

         Vysis, Inc. ("Vysis" or the "Company") is a Genomic Disease 
Management company that develops, commercializes and markets clinical 
products that provide information critical to the evaluation and management 
of cancer, prenatal disorders and other genetic diseases. Vysis currently 
markets six U.S. Food and Drug Administration ("FDA") cleared or approved 
clinical products in addition to distributing over 300 research products 
through its direct sales operations in the United States and Europe and a 
worldwide distribution network covering 51 countries. The Company has an 
installed base of over 550 proprietary genetic workstations in 32 countries. 
The Company's wholly owned subsidiary, Gene-Trak Systems Industrial 
Diagnostics Corporation, manufactures and markets food testing kits based on 
DNA ("Deoxyribonucleic Acid") probes.

         The Company was incorporated in Delaware on April 18, 1991. The 
Company's business represents the consolidation of multiple research units 
and programs of the former Amoco Corporation. On December 31, 1998, Amoco 
Corporation merged with the former British Petroleum Corporation, and as a 
result of the merger became a wholly-owned subsidiary of BP Amoco p.l.c. As 
used herein, "BP Amoco" refers to BP Amoco p.l.c. and its wholly owned 
subsidiaries. In 1994, BP Amoco began consolidation of all of its medical 
diagnostic businesses and related research under the Company. In March 1994, 
BP Amoco contributed to the Company all of its genetic disease related 
assets, including the stock of Imagenetics Incorporated (an Illinois 
corporation). Also in March 1994, BP Amoco contributed all of its infectious 
disease related assets and the stock of Gene-Trak, Inc. to the Company. 
Gene-Trak, Inc. had previously acquired certain infectious disease related 
assets from Genzyme Corporation and BP Amoco, including all of the interest 
in Gene-Trak Systems, a joint venture partnership for infectious disease 
diagnostics established by BP Amoco and Integrated Genetics in 1986.

         On February 10, 1998, the Company completed the initial public 
offering of 3 million shares of its Common Stock, par value $0.001 per share, 
at a price of $12.00 per share (the "IPO"). The net proceeds of the IPO after 
deducting expenses were approximately $32.1 million. Concurrent with the 
consummation of the IPO, the Company issued 675,000 shares of Common Stock at 
$12.00 per share to BP Amoco in exchange for a reduction of $8.1 million in 
the Company's note payable to BP Amoco. As of May 17, 1999, BP Amoco 
beneficially owns approximately 68 percent of the Company's outstanding 
Common Stock.

NOTE 2--FINANCIAL INFORMATION:

         The unaudited interim consolidated financial statements of the 
Company have been prepared pursuant to the rules and regulations of the 
Securities and Exchange 


                                    6

<PAGE>


                                   VYSIS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS--(CONTINUED)
                                   (UNAUDITED)


Commission. Accordingly, certain information and footnote disclosures 
normally included in financial statements prepared in accordance with 
generally accepted accounting principles have been condensed or omitted. 
These interim consolidated financial statements should be read in conjunction 
with the consolidated financial statements and notes thereto included in the 
Company's Annual Report on Form 10-K for the year ended December 31, 1998, as 
filed with the Securities and Exchange Commission.

         In the opinion of management, the interim consolidated financial 
statements reflect all adjustments necessary for a fair presentation of the 
interim periods. All such adjustments are of a normal, recurring nature. 
Certain amounts in fiscal 1998 have been reclassified to conform to the 
fiscal 1999 presentation. These changes had no impact on previously reported 
results of operations or stockholders' equity. The results of operations for 
the interim periods are not necessarily indicative of the results of 
operations to be expected for a full year.

NOTE 3--RECENT ACCOUNTING PRONOUNCEMENTS:

         In June 1998, the Financial Accounting Standards Board issued SFAS 
No. 133 "Accounting for Derivative Instruments and Hedging Activities," 
effective for all fiscal quarters of all fiscal years beginning after June 
15, 1999. It establishes accounting and reporting standards for derivative 
instruments and for hedging activities. It requires that an entity recognize 
all derivatives as either assets or liabilities in the statement of financial 
position and measure those instruments at fair value. The Company anticipates 
that, due to its current non-use of derivative instruments, the adoption of 
SFAS No. 133 will not have a significant effect on the Company's results of 
operations or its financial position.

NOTE 4--COMPOSITION OF BALANCE SHEET COMPONENT:

         Inventories consisted of the following (in thousands):
<TABLE>
<CAPTION>
                                          MARCH 31,    DECEMBER 31,
                                            1999         1998
                                         ----------    ------------
<S>                                      <C>           <C>
Raw materials and supplies ........        $1,339        $  900

Finished goods ....................         1,284         1,587
                                          -------       -------
                                           $2,623        $2,487
                                          -------       -------
                                          -------       -------
</TABLE>

NOTE 5--LEASE RECEIVABLES AND LONG-TERM DEBT:

        A wholly-owned foreign subsidiary of the Company has entered into 
certain sales-type leasing transactions with customers. In order to comply 
with local regulations with respect to such leasing transactions, the 
subsidiary must borrow money and has assigned to the lender a security 
interest in the lease receivables and related equipment. The debt is payable 
in monthly or quarterly installments, matures over the next three years and 


                                    7

<PAGE>


                                   VYSIS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS--(CONTINUED)
                                   (UNAUDITED)


bears interest at rates ranging from 6.4% to 9.5%. The aggregate maturities 
of gross lease receivables and long-term debt for the years ending March 31, 
are as follows:

<TABLE>
<CAPTION>
                         GROSS        LONG-TERM
                      RECEIVABLES        DEBT
                     ------------    -----------
<S>                  <C>             <C>
2000 ........          $  456          $  517
2001 ........             498             328
2002 ........             288              24
                       ------          ------
                       $1,242          $  869
                       ------          ------
                       ------          ------
</TABLE>

         The components of net lease receivables are as follows:
<TABLE>
<CAPTION>
                                                                  MARCH 31,
                                                                    1999
                                                                 ----------
          <S>                                                    <C>
          Gross lease receivables.............................     $1,242
          Allowance for doubtful accounts.....................       (322)
          Unearned income.....................................        (22)
                                                                 ----------
                                                                   $  898
                                                                 ----------
                                                                 ----------
</TABLE>

NOTE 6--RESTRUCTURING:

         On March 17, 1999, the Company's Board of Directors approved a 
restructuring plan that resulted in the elimination of 20 positions within 
the Company. The Company recorded a restructuring charge for severance costs 
of $0.5 million during the first quarter of 1999.

NOTE 7--GAIN ON SALE OF INVESTMENT:

         During the first quarter of 1999, the Company sold its 
available-for-sale investment of Incyte Pharmaceuticals, Inc. ("Incyte") 
common stock for $0.5 million, resulting in a gain on the sale of $0.4 
million.

NOTE 8--SEGMENT AND GEOGRAPHIC INFORMATION:

         The Company operates in one reportable business segment: the 
development, manufacture and sale of genetic testing products. The Company's 
revenues by product line are as follows (in thousands):




                                    8

<PAGE>

                                   VYSIS, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS--(CONTINUED)
                                   (UNAUDITED)

<TABLE>
<CAPTION>
                                                           THREE MONTHS ENDED MARCH 31,
                                                           ----------------------------
                                                             1999                1998
                                                           ---------           -------
<S>                                                        <C>                 <C>
FDA/ADM approved clinical genetic testing products........   $   881           $   446
Research and other genetic testing products ..............     2,077             1,747
Genetic instrument products ..............................     1,468             1,531
Genetic research grants and license revenue ..............       161               492
Distributed laboratory products...........................       158               220
Food testing products.....................................       699               615
                                                             -------           -------
Consolidated total revenues...............................    $5,444            $5,051
                                                             -------           -------
                                                             -------           -------
</TABLE>

         The Company's revenues by geographic area based on location of
customers are as follows (in thousands):

<TABLE>
<CAPTION>
                                              THREE MONTHS ENDED MARCH 31,
                                             -----------------------------
                                                1999              1998
                                             ---------         -----------
<S>                                          <C>               <C>
United States .........................        $ 2,506           $ 2,103
Europe, Middle East and Africa ........          3,718             3,196
Other .................................            614               495
Eliminations ..........................         (1,394)             (743)
                                               -------           -------
Consolidated total revenues ...........        $ 5,444           $ 5,051
                                               -------           -------
                                               -------           -------
</TABLE>

NOTE 9--CONTINGENCY:

         The Company and BP Amoco are defendants in a law suit pending in the 
U.S. District Court in California alleging infringement of certain patents. 
The allegedly infringing activities are the manufacture, use and sale of 
reagents and kits for detecting certain food and environmental pathogens 
currently used in the Company's food testing business. The previous stay in 
this suit has been lifted and the litigation is in the early stages of 
discovery. The Company is vigorously defending the suit. As part of the suit, 
the Company has brought a counter-claim of infringement of a patent assigned 
to the Company relating to assays for a particular pathogen due to the 
plaintiff's manufacture, use and sale of tests that detect the pathogen in 
foodstuffs. The Company has indemnified BP Amoco against damages from the 
patent infringement claims in the suit. Although the Company believes that it 
has meritorious defenses in the suit, there can be no assurance that the 
Company will ultimately prevail. An unfavorable outcome for the Company is 
considered neither probable nor remote by management. An estimate of a 
possible loss or range of a possible loss cannot currently be made. However, 
an adverse determination against the Company, which may include a finding of 
willful infringement and the awarding of plaintiff's attorney's fees, could 
have a material adverse effect on the Company's financial statements. At 
March 31, 1999, the Company has accrued estimated future minimum legal costs 
related to this matter of $0.8 million.


                                    9

<PAGE>

                                 VYSIS, INC.

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

        The following discussion and analysis provides information which 
management believes is relevant to an assessment and understanding of the 
Company's results and financial condition. The discussion should be read in 
conjunction with the audited consolidated financial statements of the Company 
and notes thereto, which were included in the Company's Annual Report on Form 
10-K for the year ended December 31, 1998 as well as the financial statements 
of the Company and notes thereto. This Quarterly Report on Form 10-Q contains 
certain statements which describe the Company's beliefs concerning future 
business conditions and the outlook for the Company based on currently 
available information. Whenever possible, the Company has identified these 
"forward-looking" statements (as defined in Section 21E of the Securities 
Exchange Act of 1934) by words such as "anticipates", believes", estimates", 
"expects", and similar expressions. These forward-looking statements are 
subject to risks and uncertainties which could cause the Company's actual 
results, performance and achievements to differ materially from those 
expressed in or implied by these statements. These risks and uncertainties 
include, but are not limited to, the following: competition; compliance by 
the Company with regulatory requirements; the ability of the Company to 
successfully market and sell its products and equipment; delays in the 
acceptance and adoption rates for the Company's clinical products; the 
Company's ability to manufacture products in sufficient quantities; the 
Company's ability to maintain intellectual property protection for its 
proprietary products, to defend its existing intellectual property rights 
from challenges by third parties, and to avoid infringing intellectual 
property rights of third parties; and the extent to which the clinicians or 
laboratories using the Company's products are able to obtain third-party 
reimbursement.

OVERVIEW

         Vysis is a leading genomic disease management company that develops, 
commercializes and markets clinical products that provide information 
critical to the evaluation and management of cancer, prenatal disorders and 
other genetic diseases. The Company currently markets clinical products 
cleared by the U.S. Food and Drug Administration ("FDA") and the French 
Agence du Medicament ("ADM"), and a line of research products, imaging 
workstations and other instruments for genetic analysis. During March 1998, 
the Company received registration from the ADM to market throughout Europe 
the AneuVysion(TM) EC Assay for Down Syndrome and other chromosomal disorders 
associated with mental retardation and birth defects. The Company has a 
pending application for registration with the ADM to market CEP(R) X/Y, 
CEP(R) 8 and CEP(R) 12 DNA Probe Kits for use as adjuncts to standard 
cytogenetic analysis to identify and enumerate the presence of chromosomes X 
and Y in bone marrow and chromosomes 8 and 12 in blood specimens, thus aiding 
in the diagnosis and treatment of leukemia patients. The Company's 
PathVysion(TM) HER-2 DNA probe kit was approved by the FDA in December 1998 
for the assessment of the HER-2 gene status in node positive Stage II breast 
cancer patients and for the prediction of the therapeutic outcome of using 
adriamycin based chemotherapy in breast cancer patients. Vysis currently 


                                    10

<PAGE>

                                 VYSIS, INC.

             MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
              CONDITION AND RESULTS OF OPERATIONS--(CONTINUED)

markets six FDA cleared clinical products, including PathVysion(TM) HER-2, 
the U.S. versions of CEP X/Y, CEP 8 and CEP 12 and AneuVysion(TM), which 
received 510(k) clearance by the FDA during 1997, and over 300 research 
products. The Company has direct sales operations in the United States and 
Europe, a marketing partnership in Japan with Fujisawa Pharmaceutical Co., 
and a worldwide distribution network.

RESULTS OF OPERATIONS

        Product revenue for the three months ended March 31, 1999 was $5.3 
million, an increase of $0.7 million, or 16%, as compared to the first 
quarter of 1998, while grant and other revenue of $0.2 million represented a 
$0.3 million decrease as compared to the prior year quarter. As a result, 
total revenues for the first quarter of 1999 were $5.4 million, an increase 
of $0.4 million, or 8%, over the prior year quarter. The product revenue 
increase in 1999 is primarily attributable to a $0.4 million, or 98%, 
increase in worldwide shipments of FDA/ADM approved clinical genetic testing 
products ("Clinical") and a $0.3 million, or 19%, increase in worldwide 
shipments of research and other genetic testing products ("Research"). For 
the first quarter of 1999, genetic instrument sales of $1.5 million declined 
4% as compared to the prior year. The increase in Clinical sales was 
primarily due to sales of the Company's PathVysion(TM) HER-2 DNA Probe Kit 
that was approved by the FDA in December 1998 and an increase in utilization 
of the Company's AneuVysion(TM) assay. The increase in Research sales was 
primarily due to a general increase in United States market demand for the 
Company's products. The slight decline in instrument sales reflects the 
continued weakness of the overall instrument market. For the three months 
ended March 31, 1999, grant and other revenue decreased $0.3 million, 
primarily due to the completion of two United States Department of Commerce 
research grants in February 1998 and July 1998.

        Cost of goods sold for the three months ended March 31, 1999 of $2.0 
million was consistent with the prior year quarter. As a percentage of 
product revenue, gross profit increased to 61.3% for the first quarter of 
1999 as compared to 54.8% for the prior year quarter, primarily due to a 
better product mix as the aforementioned significant growth in the higher 
margin Clinical and Research products represented a higher percentage of 
total product sales versus the prior year. The Company's remaining product 
lines carry significantly lower margins than the Clinical and Research 
products. For the three months ended March 31, 1999, product gross profit was 
$3.2 million, an increase of $0.7 million, or 30%, over the prior year 
quarter, primarily attributable to the increase in product revenue and gross 
margin improvement.

        Operating expenses for the three months ended March 31, 1999 were 
$7.4 million, a decrease of $0.2 million, or 2%, as compared to the first 
quarter of 1998, despite the first quarter of 1999 including a $0.5 million 
restructuring charge associated with the elimination of 20 positions. 
Research and development expenses of $2.5 million were relatively consistent 
with the first quarter of 1998. Selling, general and administrative expenses 
of $4.4 million represented a decrease of $0.6 million, or 12%, in comparison 


                                    11
<PAGE>

                                 VYSIS, INC.

             MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
              CONDITION AND RESULTS OF OPERATIONS--(CONTINUED)

to the prior year quarter. This decrease was due to a reduction in general 
and administrative expenses of $1.0 million primarily due to lower 
litigation expense, partially offset by a $0.4 million increase in selling 
expense primarily attributable to the hiring of additional sales personnel 
and marketing expenses incurred to launch the Company's December 1998 FDA 
approved PathVysion-(TM)- product.

        Interest income for the three months ended March 31, 1999 of $0.2 
million was consistent with the prior year. Interest expense decreased $0.1 
million due to the Note Payable--BP Amoco remaining outstanding until the 
completion on February 10, 1998 of the Company's IPO.

        The gain on sale of investment for the three months ended March 31, 
1999 was $0.4 million that resulted from the $0.5 million sale of the 
Company's investment in Incyte common stock.

INCOME TAXES

         Prior to the completion of the Company's IPO, the results of 
operations were included in the consolidated income tax returns of BP Amoco; 
accordingly, the domestic net operating losses through February 10, 1998 have 
been utilized by BP Amoco in its consolidated income tax returns and are not 
available to offset the Company's future taxable income. Subsequent to the 
IPO, the Company is filing separate federal income tax returns. As the 
Company was in a loss position for the three months ended March 31, 1999, no 
federal provision is recorded. For state income taxes, the Company's results 
of operations will continue to be included with BP Amoco, due to its 68 
percent ownership interest in the Company, in those states where required by 
state tax law. Under state tax laws in a number of states, including Illinois 
(the state in which much of the Company's business is taxed), the Company is 
required by law to be included in BP Amoco's unitary state tax returns as 
long as BP Amoco owns or controls 50 percent or more of the voting equity. 
For unitary state filings, the tax sharing agreement with BP Amoco requires 
BP Amoco to pay the Company the incremental tax savings, if any, received by 
BP Amoco as a result of including the Company's results of operations in such 
filings. The agreement also requires the Company to pay BP Amoco the 
incremental tax liability, if any, incurred by BP Amoco as a result of 
including the Company's results of operations in such filings. The Company 
and BP Amoco are currently unable to estimate the amount of state income tax 
benefit to be received by the Company as a result of its operating losses for 
the three months ended March 31, 1999 and, accordingly, no state tax benefit 
is recorded. For state income taxes in non-unitary states, the Company has 
not recorded any benefit as a result of its loss position for the three 
months ended March 31, 1999.

         A full valuation allowance has been provided for all deferred tax 
assets (net of liabilities) at March 31, 1999 as management does not consider 
realization of such amounts more likely than not.

                                    12

<PAGE>
                                 VYSIS, INC.

             MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
              CONDITION AND RESULTS OF OPERATIONS--(CONTINUED)

LIQUIDITY AND CAPITAL RESOURCES

        Net cash used in operating activities for the three months ended 
March 31, 1999 was $4.9 million, a decrease of $0.7 million over the prior 
year quarter, driven primarily by the reduction in operating losses during 
the first quarter of 1999 as compared to the prior year quarter.

        Net cash provided by investing activities for the three months ended 
March 31, 1999 was $3.0 million, resulting primarily from maturities of 
short-term investments. During the prior year quarter, the $8.0 million of 
net cash flows used in investing activities resulted primarily from the 
purchase of short-term investments with a portion of the net proceeds from 
the February 1998 IPO.

        Net cash used in financing activities for the three months ended 
March 31, 1999 was $0.1 million, an increase of $32.1 million from the prior 
period primarily due to receiving the net proceeds from the IPO during 
February 1998.

         At March 31, 1999, the Company had cash, cash equivalents and 
short-term investments of $13.6 million and an accumulated deficit of $52.1 
million. Since its inception, the Company has experienced negative cash flows 
from operations. In order to preserve the Company's cash position and to 
reduce cash used in operating activities, the Company's Board of Directors 
approved during March 1999 a restructuring plan that resulted in the 
elimination of 20 positions in the U.S., representing a 12 percent reduction 
of the U.S. work force, thereby reducing ongoing annual cash expenditures by 
an estimated $1.6 million. The Company recorded a restructuring charge for 
severance costs of $0.5 million during the first quarter of 1999.

        The Company believes that its current cash and short-term investment 
position, and the interest to be earned thereon, will be sufficient to fund 
the Company's operations into 2000. The Company's estimate of the time period 
for which cash funds will be adequate to fund its operations is a forward 
looking estimate subject to risks and uncertainty, and actual results may 
differ materially. The Company's requirements for additional capital will 
depend on many factors, including growth in product revenue; payments 
received under existing and potential collaborative agreements; the 
availability of government research grant payments; the progress of the 
Company's collaborative and independent research and development projects; 
the costs of preclinical and clinical trials for the Company's products; the 
prosecution, defense and enforcement of patent claims and other intellectual 
property rights; and the development of manufacturing, sales and marketing 
capabilities. To the extent capital resources, including payments from 
existing and possible future collaborative agreements and grants, together 
with the net proceeds of the IPO are insufficient to meet future capital 
requirements, the Company will have to raise additional funds to continue the 
development of its technologies. There can be no assurance that such funds 
will be available on favorable terms, or at all. To the extent that 
additional capital is raised through the sale of equity or convertible debt 


                                    13
<PAGE>

                                 VYSIS, INC.

             MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
              CONDITION AND RESULTS OF OPERATIONS--(CONTINUED)

securities, the issuance of such securities could result in dilution to the 
Company's shareholders. If adequate funds are not available, the Company may 
be required to curtail operations significantly or to obtain funds through 
entering into collaborative agreements on unattractive terms. The Company's 
inability to raise capital as and when needed would have a material adverse 
effect on the Company's business, financial condition and results of 
operations.

READINESS FOR THE YEAR 2000

         Many currently installed computer systems and software products are 
coded to accept only two digit entries in the date code field. As the Year 
2000 approaches, these code fields will need to accept four digit entries to 
distinguish years beginning with "19" from those beginning with "20". As a 
result, computer systems and/or software products used by many companies may 
need to be upgraded to comply with such Year 2000 requirements.

         The Company is in the process of evaluating the Year 2000 readiness 
of the software products sold by the Company ("Products"), the information 
technology systems used in its operations ("IT Systems"), and its non-IT 
Systems, such as manufacturing/facility related equipment and other systems 
that could impact the operations of the Company. The Company currently 
anticipates that this project will consist of the following phases: (i) 
identification of all Products, IT Systems, and non-IT Systems; (ii) 
assessment of repair or replacement requirements; (iii) repair or 
replacement; (iv) testing where necessary; (v) implementation; and (vi) 
creation of contingency plans in the event of Year 2000 failures.

         The Company completed the review of all current versions of its 
Products and believes that all Products are Year 2000 compliant. With respect 
to IT Systems, the Company has developed a plan to make its systems Year 2000 
compliant and has begun implementation of the plan during the first quarter 
of 1999. The Company's current IT Systems related to manufacturing are 
already Year 2000 compliant. To implement the other IT Systems modules for 
Year 2000 compliance requires an upgrade to a more current version of the 
existing software, which was supplied to the Company at no charge. However, 
the Company has elected to use this opportunity to upgrade all modules to the 
most current version offered by the software vendor. The Company currently 
expects this project to be substantially complete by the third quarter of 
1999. Once installed and operational, the Company will assess the need to 
develop contingency plans related to these IT Systems. The Company does not 
expect this project to have a significant impact on its information 
technology ("IT") budget or other non-related IT projects, as discussed 
below. The Company will continue to implement IT systems with strategic value 
and has started to implement a new European management information system 
which is expected to also be completed in 1999.

         In the area of non-IT Systems, the Company relies, both domestically 
and internationally, upon various vendors, government agencies, research 


                                    14
<PAGE>

                                 VYSIS, INC.

             MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
              CONDITION AND RESULTS OF OPERATIONS--(CONTINUED)

institutions, utility companies, telecommunications service companies, 
delivery service companies, and other material and service providers who are 
outside of the Company's control. There is no assurance that such parties 
will not suffer a Year 2000 business disruption, which could have a material 
adverse effect on the Company's financial condition and results of 
operations. The Company has initiated formal communications with significant 
vendors and customers to determine the extent of which the Company is 
vulnerable to those third parties' failure to remediate their own Year 2000 
issues. The Company is requesting that third party vendors represent their 
products and services to be Year 2000 compliant and that they have a program 
to test for Year 2000 compliance. However, the response of those third 
parties is beyond the Company's control. To the extent that the Company does 
not receive adequate responses by June 1999, it is prepared to develop 
contingency plans, with completion of these plans scheduled for no later than 
September 1999. At this time, the Company cannot estimate the additional 
cost, if any, that might develop from such contingency plans. With respect to 
the manufacturing/facility related equipment and other systems, the Company 
is in the process of assessing these systems for Year 2000 compliance.

         To date, the Company has not incurred any significant expenditures 
in connection with identifying or evaluating Year 2000 compliance issues. 
Most of its expenses have related to the opportunity cost of time spent by 
employees of the Company evaluating its Products, IT Systems, non-IT Systems, 
and general Year 2000 compliance matters. Absent a significant Year 2000 
compliance deficiency, the Company currently estimates that the cost to 
complete its Year 2000 compliance programs, including updating its IT System 
modules to the most current version available, will be less than $100,000 of 
expense and $75,000 of capitalized costs.

        Breakdowns in the Company's IT Systems and non-IT Systems, such as 
its manufacturing application software and the computer chips embedded in its 
plant equipment, as well as other Year 2000-related problems such as 
disruptions in the delivery of materials, power, heat or water to the 
Company's facilities, could prevent the Company from being able to 
manufacture and ship its products. If the Company were to fail to correct a 
material Year 2000 problem, its normal business activities and operations 
could be interrupted. Such interruptions could materially and adversely 
affect the Company's results of operations, liquidity and financial condition.

         ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT 
                             MARKET RISK

         The Company is subject to market risk associated with changes in 
foreign currency exchange rates and interest rates. The Company's exchange 
rate risk is limited to its operations in England, Germany, France and Italy. 
The exchange rate risk is mitigated through local purchases for the majority 
of their expenditures. The Company's primary foreign currency exchange rate 
risk results from the foreign operations' intercompany purchases of clinical 
and research products as well as certain instrument system components. The 


                                    15

<PAGE>

                                 VYSIS, INC.

             MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
              CONDITION AND RESULTS OF OPERATIONS--(CONTINUED)

majority of the intercompany purchases are not expected to be repaid in the 
foreseeable future as these operations have required more working capital as 
a result of their significant growth. Sales throughout the rest of the world 
are denoted in U.S. dollars. The Company does not believe that the impact 
from foreign currency exchange rate fluctuations will have a material impact 
on its financial statements. The net impact of foreign exchange activities on 
earnings was immaterial for the three months ended March 31, 1999 and 1998. 
The foreign currency translation loss included in shareholders' equity 
resulting from the translation of the financial statements of the Company's 
international subsidiaries into U.S. dollars increased by $0.3 million in the 
first quarter of 1999 due to the strengthening of the U.S. dollar against the 
functional currency of the Company's international subsidiaries. Interest 
rate exposure is primarily limited to the $10.9 million of short-term 
investments owned by the Company. Such securities are debt instruments which 
generate interest income for the Company on excess cash balances. The Company 
does not actively manage the risk of interest rate fluctuations; however, 
such risk is mitigated by the relatively short term, less than 12 months, 
nature of these investments.

         The Company does not consider the present rate of inflation to have a
significant impact on its business.


                           PART II. OTHER INFORMATION

                            ITEM 1. LEGAL PROCEEDINGS

         Reference is made to Item 3. Legal Proceedings in the Company's 
Annual Report on Form 10-K for the fiscal year ended December 31, 1998 for 
discussion of litigation matters relating to the Company. The Company, BP 
Amoco and other parties have been named as defendants in a suit brought by 
Gen-Probe in the United States District Court in the Southern District of 
California (San Diego). The suit alleges direct infringement of the Kohne 
Patents by the Company's subsidiaries Gene-Trak, Inc. and Gene-Trak Systems 
Industrial Diagnostics and inducement of infringement by the Company and BP 
Amoco. The Company denies infringement and intends to vigorously contest the 
action. The Company is defending and indemnifying the claims against BP Amoco 
pursuant to an agreement between the two companies. The Company has also 
filed a counter-claim against Gen-Probe for infringement of the Company's 
U.S. Patent No. 5,089,386. The litigation is at an early stage and trial is 
scheduled to occur in about May 2000.

         The Company and other parties have been named as defendants in a 
suit pending in California state court by D.E. Kohne, the named inventor of 
the Kohne Patents. The suit alleges that the Company participated maliciously 
in the prosecution of two separate lawsuits challenging Gen-Probe's title in 
the Kohne Patents. The Company is being defended and indemnified by BP Amoco, 
also a defendant in the suit, pursuant to an agreement between the two 
companies. Discovery is ongoing. This case and a similar case brought by 
Gen-Probe against BP Amoco are expected to be tried in mid summer 1999.

                                    16

<PAGE>

                                   VYSIS, INC.

                         OTHER INFORMATION--(CONTINUED)

                ITEM 2. CHANGES IN SECURITIES AND USE OF PROCEEDS

        In connection with the IPO (see Note 1 of the Notes to Consolidated 
Financial Statements for further discussion), the Company received net 
proceeds of $32.1 million from the sale of 3,000,000 shares of its Common 
Stock. From the closing date of the IPO, February 10, 1998, to March 31, 
1999, the Company used such net offering proceeds as follows (in millions):

<TABLE>
<CAPTION>
<S>                                                                                              <C>
Purchase of short-term investments and cash equivalents ...................................      $  13.6
Repayment of note payable-BP Amoco ........................................................          2.0
Acceleration of product development, expansion of sales and 
    marketing capabilities and funding of increased working capital 
    requirements and ongoing operations....................................................         16.5
                                                                                                 -------
Total ....................................................................................       $  32.1
                                                                                                 -------
                                                                                                 -------
</TABLE>

        Each of these amounts is a reasonable estimate of the application of the
net offering proceeds. This use of proceeds does not represent a material change
in the use of proceeds described in the Prospectus for the IPO. Other than the
repayment of a note payable to BP Amoco in the amount of $2 million, none of
such amounts (with the exception of salaries and directors' fees and working
capital advances to affiliates incurred in the ordinary course of business)
represented direct or indirect payments to (i) directors or officers of the
Company or their associates, (ii) persons owning 10% or more of any class of
equity securities of the Company or (iii) affiliates of the Company.

                    ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

EXHIBITS

        Exhibit 27.1, Financial Data Schedule (included only in the electronic
filing of this document).

REPORTS ON FORM 8-K

        On January 7, 1999, the Company filed a Form 8-K with respect to the
Company's change in auditors for the fiscal 1998 examination. There were no
other Form 8-K reports filed during the quarter.


                                    17

<PAGE>



                                   VYSIS, INC.

                                    SIGNATURE

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

                                 VYSIS, INC.

Date:  May 17, 1999              By:         /s/ ALFRED H. ELLSWORTH
                                         --------------------------------------
                                         Name:  Alfred H. Ellsworth
                                         TITLE: VICE PRESIDENT, FINANCE
                                                AND CHIEF ACCOUNTING OFFICER

                                    18