<PAGE>   1
================================================================================
                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM 10-Q

(Mark One)

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

    For the quarterly period ended March 31, 1998

                                       OR

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

    For the transition period from ___________to _________

                         Commission file number 0-28194

                               DIGENE CORPORATION
             ------------------------------------------------------
             (Exact name of registrant as specified in its charter)

<TABLE>
<S>                                      <C>

             DELAWARE                                 52-1536128
-------------------------------          ------------------------------------
(State or other jurisdiction of          (I.R.S. Employer Identification No.)
incorporation or organization)


     9000 VIRGINIA MANOR ROAD
       BELTSVILLE, MARYLAND                            20705
----------------------------------------             ----------
(Address of principal executive offices)             (Zip Code)
</TABLE>

Registrant's telephone number, including area code (301) 470-6500
                                                   --------------

                                 NOT APPLICABLE
              ----------------------------------------------------
              (Former name, former address and former fiscal year,
                          if changed since 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
                                             ---   ---

    Indicate the number of shares outstanding of each of the issuer's classes of
common stock, as of the latest practicable date.
<TABLE>
<S>                                                  <C>
                                                     Shares outstanding as of
               Class                                      May 13, 1998
 --------------------------------------                -----------------
 Common Stock, par value $.01 per share                    14,117,308
</TABLE>

================================================================================
<PAGE>   2



                               DIGENE CORPORATION

                               INDEX TO FORM 10-Q

                                                                           Page

PART I.  CONSOLIDATED FINANCIAL INFORMATION:

      Item 1.  Consolidated Financial Statements -

           Consolidated Balance Sheets -

                 March 31, 1998 and June 30, 1997                            1

           Consolidated Statements of Operations -

                 Three months ended March 31, 1998 and 1997;                 2
                 Nine months ended  March 31, 1998 and 1997

           Consolidated Statements of Cash Flows -

                 Nine months ended March 31, 1998 and 1997                   3

           Notes to Consolidated Financial Statements                        4

      Item 2.  Management's Discussion and Analysis of Financial
               Condition and Results of Operations                           5

PART II.  OTHER INFORMATION:

      Item 2.  Changes in Securities and Use of Proceeds                     8

      Item 6.  Exhibits and Reports on Form 8-K                              9

SIGNATURES                                                                  10

EXHIBIT INDEX                                                               11


<PAGE>   3


PART I.  CONSOLIDATED FINANCIAL INFORMATION

                               DIGENE CORPORATION
                           CONSOLIDATED BALANCE SHEETS
<TABLE>
<CAPTION>

                                                                                  MARCH 31,        JUNE 30,
                                                                                    1998             1997
                                                                                -------------     -----------
                                                                                 (UNAUDITED)         (NOTE)
<S>                                                                               <C>             <C>     
                          ASSETS
Current assets:
   Cash and cash equivalents                                                      $19,016,237     $ 8,452,864
   Short-term investments                                                          11,315,374      11,061,283
   Accounts receivable, less allowance of approximately $61,000 at                  1,677,311       1,767,682
      March 31, 1998 and June 30, 1997, respectively
   Due from related party                                                           1,552,333       2,395,792
   Inventories                                                                      4,118,251       2,425,167
   Prepaid expenses and other current assets                                          302,362         446,368
                                                                                  -----------     -----------

Total current assets                                                               37,981,868      26,549,156

Property and equipment, net                                                         2,535,544       1,214,548
Intangible assets, net                                                              1,929,950       2,308,641
Deposits                                                                              108,094         134,564
                                                                                  ------------    -----------

Total assets                                                                      $42,555,456     $30,206,909
                                                                                  ===========     ===========


           LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
   Accounts payable                                                               $1,828,172      $2,093,893
   Accrued expenses                                                                  649,491         772,037
   Accrued payroll                                                                 1,134,321         602,555
   Due to related party                                                                    -         443,332
   Current maturities of long-term debt                                              824,897       1,338,220
                                                                                  ------------    -----------
Total current liabilities                                                          4,436,881       5,250,037

Long-term debt, less current maturities                                              342,787         552,733
Accrued rent                                                                          66,331         100,618
Deferred rent                                                                         18,314          37,318

Stockholders' equity:
   Common stock, $.01 par value, 50,000,000 shares authorized, 13,971,965
      and 11,579,530 shares issued and outstanding at March 31, 1998
      and June 30, 1997, respectively                                                139,720         115,795
   Additional paid-in capital                                                     70,302,472      49,477,621
   Accumulated deficit                                                           (32,751,049)    (25,327,213)
                                                                                 -------------  -------------

Total stockholders' equity                                                        37,691,143      24,266,203
                                                                                 -------------  ------------

Total liabilities and stockholders' equity                                       $42,555,456    $ 30,206,909
                                                                                 ===========    ============
</TABLE>


Note: The balance sheet at June 30, 1997 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 audited financial statements.

                                       1
<PAGE>   4



                               DIGENE CORPORATION
                      CONSOLIDATED STATEMENTS OF OPERATIONS
<TABLE>
<CAPTION>
                                         THREE MONTHS ENDED              NINE MONTHS ENDED
                                              MARCH 31,                      MARCH 31,

                                     ----------------------------   ----------------------------
                                         1998           1997            1998           1997
                                     -------------  -------------   -------------  -------------
<S>                                   <C>            <C>             <C>            <C>
    Revenues:
       Product sales                  $ 3,231,388    $ 2,418,339     $ 8,687,625    $ 6,237,029
       Research and development
         contracts                              -         99,536          26,500        493,694
                                      -------------  -------------   -------------  -------------

    Total revenues                      3,231,388      2,517,875       8,714,125      6,730,723

    Costs and expenses:
       Cost of product sales              970,594        884,712       2,519,843      2,433,498
       Research and development         1,518,899      1,049,803       3,797,881      2,784,720
       Selling and marketing            2,996,807      1,120,323       6,595,737      2,976,457
       General and administrative       1,354,211      1,453,995       3,606,877      3,213,711
       Amortization of intangible
         assets                           125,192         91,440         383,013        107,842
                                      -------------  -------------   -------------  -------------

    Loss from operations               (3,734,315)    (2,082,398)     (8,189,226)    (4,785,505)

    Other income (expense):
       Other income (expense)             (58,999)       (37,532)       (144,339)       (67,561)
       Interest income                    416,497        373,879       1,028,293      1,206,478
       Interest expense                   (34,728)       (32,029)       (118,564)       (35,904)
                                     -------------  -------------   -------------  -------------
    Net loss                         $ (3,411,545)  $ (1,778,080)   $ (7,423,836)  $ (3,682,492)
                                     =============  =============   =============  =============
    Basic and diluted net loss       $      (0.25)  $      (0.16)   $      (0.57)  $      (0.32)
       per share                     =============  =============   =============  =============
    Weighted average shares            13,908,214      11,418,954      12,961,727     11,346,234
       outstanding                   =============  =============   =============  =============
</TABLE>
                                       2
<PAGE>   5



                               DIGENE CORPORATION
                      CONSOLIDATED STATEMENTS OF CASH FLOWS
<TABLE>
<CAPTION>
                                                                                      NINE MONTHS ENDED
                                                                                          MARCH 31,
                                                                                -------------------------------
                                                                                     1998             1997
                                                                                --------------    -------------
                                                                                           (UNAUDITED)
<S>                                                                             <C>               <C>
OPERATING ACTIVITIES
   Net loss                                                                     $ (7,423,836)     $ (3,682,492)
   Adjustments to reconcile net loss to net cash used in
      operating activities:
      Depreciation and amortization of property and equipment                        553,183           327,443
      Amortization of intangible assets                                              383,014           107,842
      Changes in operating assets and liabilities:
         Accounts receivable                                                          90,371          (546,212)
         Due from related party                                                      843,459        (1,039,958)
         Inventories                                                              (1,693,084)         (123,620)
         Prepaid expenses and other current assets                                   144,006            93,764
         Deposits                                                                     26,470           (43,847)
         Accounts payable                                                           (265,721)         (832,206)
         Accrued expenses                                                           (122,546)          224,723
         Accrued payroll                                                             531,766           299,544
         Due to related party                                                       (443,332)          178,333
         Accrued rent                                                                (34,287)          (38,147)
         Deferred rent                                                               (19,004)          (18,361)
                                                                                -------------     -------------
Net cash used in operating activities                                             (7,429,541)       (5,093,194)

INVESTING ACTIVITIES

   Purchases of short-term investments                                           (11,496,883)      (11,035,962)
   Maturities of short-term investments                                           11,242,792         3,959,266
   Capital expenditures                                                           (1,874,179)         (775,776)
   Additions to intangible assets                                                     (4,323)       (2,498,539)
                                                                                -------------     -------------

Net cash used in investing activities                                             (2,132,593)      (10,351,011)

FINANCING ACTIVITIES

   Net proceeds from issuance of Common Stock                                     20,654,415                 -
   Exercise of Common Stock options                                                  194,361            91,449
   Proceeds from notes payable                                                             -         3,330,351
   Principal repayments on long-term debt                                           (723,269)       (1,535,813)
                                                                                -------------     -------------

Net cash provided by financing activities                                         20,125,507         1,885,987
                                                                                -------------     -------------

Net increase (decrease) in cash and cash equivalents                              10,563,373       (13,558,218)
Cash and cash equivalents at beginning of period                                   8,452,864        24,107,325

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

Cash and cash equivalents at end of period                                      $ 19,016,237      $ 10,549,107
                                                                                ============      ============
</TABLE>

                                       3
<PAGE>   6



                               DIGENE CORPORATION
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS



1.  BASIS OF PRESENTATION

The consolidated financial statements for the three month and nine month periods
ended March 31, 1998 and 1997 are unaudited and include all adjustments which,
in the opinion of management, are necessary to present fairly the results of
operations for the periods then ended. All such adjustments are of a normal
recurring nature. These consolidated financial statements should be read in
conjunction with the Annual Report on Form 10-K for the year ended June 30, 1997
of Digene Corporation (the "Company"), which includes financial statements and
notes thereto for the years ended June 30, 1997, 1996 and 1995.

The results of the Company's operations for any interim period are not
necessarily indicative of the results of the Company's operations for any other
interim period or for a full fiscal year.

2.   NET LOSS PER SHARE

In 1997, the Financial Accounting Standards Board issued Statement of Financial
Accounting Standards No. 128, Earnings Per Share. Statement 128 replaced the
previously reported primary and fully diluted earnings per share with basic and
diluted earnings per share. Unlike primary earnings per share, basic earnings
per share excludes any dilutive effects of options, warrants, and convertible
securities. Diluted earnings per share is very similar to the previously
reported fully diluted earnings per share. All earnings per share amounts for
all periods have been presented, and where necessary, restated to conform to the
Statement 128 requirements.

3.   PUBLIC OFFERING

On October 20, 1997, the Company completed a public offering of 2,250,000 shares
of its common stock, the net proceeds of which, after underwriters' commissions
and expenses, were $20,654,000.


                                       4
<PAGE>   7


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


FORWARD LOOKING STATEMENTS.

Statements regarding Digene Corporation's (the "Company") expectations as to
financial results and other aspects of its business set forth below or otherwise
made in writing or orally by the Company may constitute forward looking
statements within the meaning of the Private Securities Litigation Reform Act of
1995. Although the Company believes that its expectations are based on
reasonable assumptions within the bounds of its knowledge of its business and
operations, there can be no assurance that actual results will not differ
materially from its expectations. Factors which could cause actual results to
differ from expectations include, but are not limited to, uncertainty of future
profitability, uncertainty of clinical trial results, uncertainty of market
acceptance, risks inherent in international transactions, dependence on third
party reimbursement, competition, dependence on European distributor, extent of
government regulations, and the uncertainty regarding patents and proprietary
rights.

RESULTS OF OPERATIONS

Product sales increased to $3,231,000 and $8,688,000 for the three and nine
month periods ended March 31, 1998, respectively, from $2,418,000 and $6,237,000
for the corresponding periods in 1997. The increase was due, primarily, to
increased sales of the Company's HPV, CMV and HIV tests.

Research and development contract revenues decreased to $0 and $27,000 for the
three and nine month periods ended March 31, 1998, respectively, from $100,000
and $494,000 for the corresponding periods in 1997. The decrease was due,
primarily, to the completion of funding under certain contracts.

Cost of product sales increased to $971,000 and $2,520,000 for the three and
nine month periods ended March 31, 1998, respectively, from $885,000 and
$2,433,000 for the corresponding periods in 1997. Gross margin on product sales
increased to 70% and 71% for the three and nine month periods ended March 31,
1998, respectively, from 63% and 61%, respectively, for the corresponding
periods in 1997. This increase was due, primarily, to increased overhead
absorption (notwithstanding increases in total overhead costs), increased sales
of higher-margin Hybrid Capture products and increased product pricing.

Research and development expenses increased to $1,519,000 and $3,798,000 for the
three and nine month periods ended March 31, 1998, respectively, from $1,050,000
and $2,785,000 for the corresponding periods in 1997. The increase was due,
primarily, to the hiring of additional personnel and the related incidental
expenses to develop additional tests using the Hybrid Capture technology and to
improve the sensitivity and ease of use of that technology.



                                        5
<PAGE>   8


Selling and marketing expenses increased to $2,997,000 and $6,596,000 for the
three and nine month periods ended March 31, 1998, respectively, from $1,120,000
and $2,976,000 for the corresponding periods in 1997. The increase was due,
primarily, to substantial increases in sales and marketing programs and to the
hiring of additional selling and marketing personnel in conjunction with the
Company's efforts to increase product sales.

General and administrative expenses decreased to $1,354,000 for the three month
period ended March 31, 1998 from $1,454,000 for the corresponding period in 1997
and increased to $3,607,000 for the nine month period ended March 31, 1998 from
$3,214,000 for the corresponding period in 1997. The decrease for the three
month period ended March 31, 1998 relates to set-up costs expensed in the prior
year associated with the Company's expansion into the European market which were
non-recurring. The increase for the nine months ended March 31, 1998 was due,
primarily, to the hiring of additional administrative personnel to support the
Company's growth objectives, as well as increased overhead associated with the
Company's European expansion.

Amortization of intangible assets increased to $125,000 and $383,000 for the
three and nine month periods ended March 31, 1998, respectively, from $91,000
and $108,000 for the corresponding periods in 1997. The increase was due to
amortization of intangibles acquired in February 1997.

Interest income increased to $416,000 for the three month period ended March 31,
1998 from $374,000 for the corresponding period in 1997 and decreased to
$1,028,000 for the nine month period ended March 31, 1998 from $1,206,000 for
the corresponding period in 1997. The decrease was due to a decline in the
average investment balances resulting from the Company's use of invested funds
for working capital purposes, notwithstanding the receipt of net proceeds of
$20,654,000 from the Company's public offering of 2,250,000 shares of its common
stock in October 1997.

Interest expense increased to $35,000 and $119,000 for the three and nine month
periods ended March 31, 1998, respectively, from $32,000 and $36,000 for the
corresponding periods in 1997. The increase was due to an increase in
indebtedness in February 1997.

LIQUIDITY AND CAPITAL RESOURCES

Since inception, the Company's expenses have significantly exceeded its
revenues, resulting in accumulated deficit of approximately $32,751,000 at March
31, 1998. The Company has funded its operations primarily through the sale of
equity securities. The Company has experienced negative cash flows from
operations of $7,430,000 and $5,093,000 for the nine months ended March 31,
1998, and 1997, respectively.

Capital expenditures increased to $1,874,000 for the nine months ended March 31,
1998 from $776,000 for the corresponding period in 1997, due, primarily, to the
build-up of operations in Europe.



                                        6
<PAGE>   9


The Company does not have any bank financing arrangements. The Company's
indebtedness consists, primarily, of notes payable related to its expansion into
the European market.

The Company is assessing whether its systems, equipment and facilities present
any Year 2000 issues which may affect the Company. The Company also plans to
assess whether its material customers, suppliers and service providers are Year
2000 compliant. No determination has yet been made whether any such issues would
have a material adverse effect on the Company's business, financial condition or
results of operations.

On October 20, 1997, the Company completed a public offering of 2,250,000 shares
of its common stock, the net proceeds of which, after underwriters' commissions
and expenses, were $20,654,000.

The Company has incurred negative cash flows from operations since its
inception, and has expended, and expects to continue to expend in the future,
substantial funds to complete its planned product development efforts, expand
its sales and marketing activities and expand its manufacturing capabilities.
The Company expects that its existing capital resources, together with the net
proceeds of the Company's recent public offering and the interest thereon, will
be adequate to fund the Company's operations through 1999. No assurances can be
given that there will be no changes in the Company that would consume a
significant amount of its available resources before that time. The Company's
future capital requirements and the adequacy of available funds will depend on
numerous factors, including the successful commercialization of its products,
progress in its product development efforts, the magnitude and scope of such
efforts, progress with preclinical studies and clinical trials, progress in its
regulatory affairs activities, the cost and timing of expansion of manufacturing
capabilities, the expansion of the Company's direct European sales operations,
the development and maintenance of effective sales and marketing activities, the
cost of filing, prosecuting, defending and enforcing patent claims and other
intellectual property rights, competing technological and market developments,
and the development of strategic alliances for the marketing of its products. To
the extent that the Company's existing capital resources and funds generated
from the Company's operations, together with its existing capital resources and
the proceeds of the Company's recent public offering and the interest earned
thereon, are insufficient to meet current or planned operating requirements, the
Company will be required to obtain additional funds through equity or debt
financing, strategic alliances with corporate partners and others, or through
other sources. The terms and prices of any equity or debt financings may be
significantly more favorable to investors than those of the Common Stock sold in
the Company's recent public offering. The Company does not have any committed
sources of additional financing, and there can be no assurance that additional
funding, if necessary, will be available on acceptable terms, if at all. If
adequate funds are not available, the Company may be required to delay, scale
back or eliminate certain aspects of its operations or attempt to obtain funds
through arrangements with collaborative partners or others that may require the
Company to relinquish rights to certain of its technologies, product candidates,
products or potential markets. If adequate funds are not available, the
Company's business, financial condition and results of operations will be
materially and adversely effected.


                                       7

<PAGE>   10


PART II. OTHER INFORMATION

Item 2.  Changes in Securities and Use of Proceeds

Effective date of the registration for which the
use of proceeds information is being disclosed:            May 21, 1996

SEC file number assigned to the registration statement:    0-28194

Offering commencement date:                                May 22, 1996
(Offering was not terminated before the sale of
 all securities registered)

Names of managing underwriters:                            UBS Securities LLC
                                                           Montgomery Securities

Title of security:                                         Common Stock, par
                                                           value $.01 per share


<TABLE>
<S>                                                                 <C>         
FOR THE ACCOUNT OF THE ISSUER

Amount registered                                                      3,000,000
Aggregate price of offering amount registered                       $ 34,500,000
Amount sold                                                            3,000,000
Aggregate offering price of amount sold                             $ 34,500,000

DIRECT OR INDIRECT PAYMENTS TO OTHERS FOR:

Underwriting discounts and commissions                              $  2,415,000
Other expenses                                                      $  1,180,000
                                                                    ------------
TOTAL EXPENSES                                                      $  3,595,000

NET OFFERING PROCEEDS TO THE ISSUER                                 $ 30,905,000

DIRECT OR INDIRECT PAYMENTS TO OTHERS FOR:

Construction of plant, building and facilities                      $    327,000
Purchases and installations of machinery and equipment              $  2,533,000
Repayment of indebtedness                                           $  2,924,000
Working capital                                                     $ 14,820,000

Temporary investments

Option Market Preferred Stock                                       $    500,000
Corporate Bonds                                                     $  4,048,000
Commercial Paper                                                    $  3,051,000

Other purposes

Payments re:  Murex Agency Agreement                                $  2,702,000

                                                                    ------------
TOTAL                                                               $ 30,905,000
</TABLE>



                                        8
<PAGE>   11


Item 6.  Exhibits and Reports on Form 8-K

(a)  Exhibits

3.1    Amended and Restated Certificate of Incorporation (Incorporated
       by reference to Exhibit 3.1 to the Company's Registration Statement
       on Form S-1 (File No. 333-2968))

3.2    Amended and Restated Bylaws (Incorporated by reference to Exhibit 3.2 to
       the Company's Registration Statement on Form S-1 (File No. 333-2968))

4.1    Form of Common Stock Certificate (Incorporated by reference to Exhibit
       4.1 to the Company's Registration Statement on Form S-1 (File No.
       333-2968))

10.1   Lease by an between ARE-Metropolitan Grove I, LLC and the company, 
       dated as of March 2, 1998.
                                
27     Financial Data Schedule

(b)    Reports on Form 8-K

The Company did not file any reports on Form 8-K during the quarter ended March
31, 1998.


                                        9
<PAGE>   12

                                   SIGNATURES

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.



                                                      DIGENE CORPORATION


Date:          May 1, 1998                 By:  /s/  Charles M. Fleischman
     -------------------------------          ----------------------------------
                                                     Charles M. Fleischman
                                                   Executive Vice President,
                                                    Chief Operating Officer,
                                                    Chief Financial Officer
                                                 (Principal Financial Officer)

Date:          May 1, 1998                     By:  /s/  Joseph P. Slattery
     ------------------------------               ------------------------------
                                                         Joseph P. Slattery
                                                             Controller
                                                  (Principal Accounting Officer)


                                       10

<PAGE>   13



                                  EXHIBIT INDEX

<TABLE>
<S>                <C>                                                                 <C>
Exhibit No.        Description                                                         Page

   3.1             Amended and Restated Certificate of Incorporation
                   (Incorporated by reference to Exhibit 3.1 to the Company's
                   Registration Statement on Form S-1 (File No. 333-2968))

   3.2             Amended and Restated Bylaws (Incorporated by reference
                   to Exhibit 3.2 to the Company's Registration Statement on
                   Form S-1 (File No. 333-2968))

   4.1             Form of Common Stock Certificate (Incorporated by reference
                   to Exhibit 4.1 to the Company's Registration Statement on
                   Form S-1 (File No. 333-2968))

   10.1            Lease by and between ARE-Metropolitan Grove I, LLC and the
                   Company, dated as of MArch 2, 1998. 

   27              Financial Data Schedule
</TABLE>

                                       11