<PAGE>
                                  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 June 30, 2004 OR

    [ ] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES
        EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD          to         .
                                                       --------    --------

                        COMMISSION FILE NUMBER: 000-31745

                          THIRD WAVE TECHNOLOGIES, INC.
             (Exact name of Registrant as specified in its charter)

            DELAWARE                                         39-1791034
    (State or other jurisdiction                          (I.R.S. Employer
  of incorporation or organization)                      Identification No.)

    502 S. ROSA ROAD, MADISON, WI                               53719
(Address of principal executive offices)                      (Zip Code)

                                 (888) 898-2357
              (Registrant's telephone number, including area code)

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 by check whether the Registrant is an accelerated filer (as defined in
Exchange Act Rule 12b-2 of the Exchange Act). Yes [X] No [ ]

The number of shares outstanding of the registrant's Common Stock, $.001 par
value, as of June 30, 2004, was 40,446,409.


<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.
                          QUARTERLY REPORT ON FORM 10-Q
                       FOR THE QUARTER ENDED JUNE 30, 2004

                                TABLE OF CONTENTS
<Table>
<Caption>
                                                                                 PAGE NO.
<S>                                                                             <C>
PART I FINANCIAL INFORMATION........................................................  3
   Item 1. Financial Statements.....................................................  3
      Consolidated Balance Sheets as of June 30, 2004 and December 31, 2003.........  3
      Consolidated Statements of Operations for the three and six months
        ended June 30, 2004 and 2003................................................  4
      Consolidated Statements of Cash Flows for the six months ended June 30,
        2004 and 2003...............................................................  5
      Notes to Consolidated Financial Statements....................................  6
   Item 2. Management's Discussion and Analysis of Financial Condition and
        Results of Operations.......................................................  9
   Item 3. Quantitative and Qualitative Disclosures About Market Risk............... 13
   Item 4. Controls and Procedures.................................................. 13
PART II OTHER INFORMATION........................................................... 14
   Item 1. Legal Proceedings........................................................ 14
   Item 2. Changes In Securities, Use Of Proceeds, and Issuer Purchases of Equity
        Securities.................................................................. 14
   Item 3. Defaults Upon Senior Securities.......................................... 14
   Item 4. Submission Of Matters To A Vote Of Security Holders...................... 14
   Item 5. Other Information........................................................ 15
   Item 6. Exhibits And Reports On Form 8-K......................................... 15
SIGNATURES.......................................................................... 15
EXHIBITS............................................................................
</Table>

                                       2

<PAGE>


                         PART I - FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

                          THIRD WAVE TECHNOLOGIES, INC.
                           Consolidated Balance Sheets

<Table>
<Caption>
                                                                           JUNE 30, 2004      DECEMBER 31, 2003
                                                                            UNAUDITED
<S>                                                                        <C>              <C>
ASSETS
Current assets:
  Cash and cash equivalents                                                $  58,197,612    $         47,015,746
  Short-term investments                                                      10,800,000              10,800,000
  Receivables, net of allowance for doubtful accounts of
   $140,000 at June 30, 2004 and December 31, 2003                             3,228,773               2,061,054
  Inventories                                                                  1,922,788               1,394,046
  Prepaid expenses and other                                                     702,778                 485,680
                                                                           -------------    --------------------
Total current assets                                                          74,851,951              61,756,526
Equipment and leasehold improvements:
  Machinery and equipment                                                     15,558,444              18,544,956
  Leasehold improvements                                                       2,032,791               2,099,104
                                                                           -------------    --------------------
                                                                              17,591,235              20,644,060
  Less accumulated depreciation                                               11,232,045              12,116,813
                                                                           -------------    --------------------
                                                                               6,359,190               8,527,247
Assets held for sale                                                             312,000                       0
Intangible assets, net of accumulated amortization                             4,898,748               5,651,124
Indefinite lived intangible assets                                             1,007,411               1,007,411
Goodwill                                                                         489,873                 489,873
Other long term assets                                                         2,549,418               2,989,752
                                                                           -------------    --------------------
Total assets                                                               $  90,468,591    $         80,421,933
                                                                           =============    ====================

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities:
  Accounts payable                                                         $   5,653,085    $          4,955,434
  Accrued payroll and related liabilities                                      2,007,591               2,802,297
  Other accrued liabilities                                                    1,241,999               1,776,250
  Deferred revenue                                                             5,395,419                  67,760
  Long-term debt due within one year                                           9,558,481               9,500,000
                                                                           -------------    --------------------
Total current liabilities                                                     23,856,575              19,101,741
Long-term debt                                                                   154,852                  13,333
Deferred revenue - long term                                                     247,917                       0
Other liabilities                                                              2,793,789               2,019,024
Shareholders' equity:
  Participating preferred stock, Series A, $.001 par value,
   10,000,000 shares authorized, 0 shares issued and outstanding                       0                       0
  Common stock, $.001 par value, 100,000,000 shares authorized,
   40,446,409 and 40,021,244 shares issued and outstanding, respectively          40,446                  40,021
  Additional paid-in capital                                                 194,892,151             193,356,121
  Unearned stock compensation                                                   (461,692)               (309,996)
  Foreign currency translation adjustment                                         33,478                  33,307
  Accumulated deficit                                                       (131,088,925)           (133,831,618)
                                                                           -------------    --------------------
Total shareholders' equity                                                    63,415,458              59,287,835
                                                                           -------------    --------------------
Total liabilities and shareholders' equity                                 $  90,468,591    $         80,421,933
                                                                           =============    ====================
</Table>

                 See accompanying notes to financial statements.




                                       3
<PAGE>



                          THIRD WAVE TECHNOLOGIES, INC.

                      Consolidated Statements of Operations
                                   (Unaudited)

<Table>
<Caption>
                                         THREE MONTHS ENDED JUNE 30,      SIX MONTHS ENDED JUNE 30,
                                        ----------------------------    ----------------------------
                                            2004            2003            2004            2003
                                        ------------    ------------    ------------    ------------
<S>                                     <C>             <C>             <C>             <C>
Revenues:
     Product sales                      $ 12,543,461    $  8,515,318    $ 27,758,099    $ 16,701,055
     Development revenue                           0         250,000               0         500,000
     License and royalty revenue              40,404          28,028          81,045          53,600
     Grant revenue                            48,402          23,875          68,732          54,457
                                        ------------    ------------    ------------    ------------
Total revenues                            12,632,267       8,817,221      27,907,876      17,309,112
                                        ------------    ------------    ------------    ------------
Operating expenses:
     Cost of goods sold
        Product cost of goods sold         2,948,652       2,884,950       6,449,405       5,487,216
        Intangible and long-term
          asset amortization                 541,561         490,296       1,112,657         977,201
                                        ------------    ------------    ------------    ------------
     Total cost of goods sold              3,490,213       3,375,246       7,562,062       6,464,417

     Research and development              3,363,377       2,912,297       6,307,540       5,831,575
     Selling and marketing                 2,696,218       2,520,489       5,320,991       4,861,432
     General and administrative            3,079,591       2,246,009       5,264,702       5,416,776
     Impairment charge                       758,716               0         758,716               0
                                        ------------    ------------    ------------    ------------
Total operating expense                   13,388,115      11,054,041      25,214,011      22,574,200
                                        ------------    ------------    ------------    ------------
Income (loss) from operations               (755,848)     (2,236,820)      2,693,865      (5,265,088)
Other income (expense):
     Interest income                         142,758         160,271         269,948         331,066
     Interest expense                        (58,755)        (92,000)       (115,749)       (184,083)
     Other                                   566,115           7,804        (105,371)         33,535
                                        ------------    ------------    ------------    ------------
Other income                                 650,118          76,075          48,828         180,518
                                        ------------    ------------    ------------    ------------
Net income (loss)                       $   (105,730)   $ (2,160,745)   $  2,742,693    $ (5,084,570)
                                        ============    ============    ============    ============

Net income (loss) per share - basic     $      (0.00)   $      (0.05)   $       0.07    $      (0.13)
                                        ============    ============    ============    ============
Net income (loss) per share - diluted   $      (0.00)   $      (0.05)   $       0.07    $      (0.13)
                                        ============    ============    ============    ============
Weighted Average Shares outstanding
       Basic                              40,325,351      39,699,313      40,201,932      39,631,630
                                        ============    ============    ============    ============
       Diluted                            40,325,351      39,699,313      41,874,808      39,631,630
                                        ============    ============    ============    ============
</Table>

                 See accompanying notes to financial statements.



                                       4
<PAGE>



                          THIRD WAVE TECHNOLOGIES, INC.

                      Consolidated Statements of Cash Flows
                                   (Unaudited)

<Table>
<Caption>
                                                                            SIX MONTHS ENDED
                                                                                JUNE 30,
                                                                     ----------------------------
                                                                          2004            2003
                                                                     ------------    ------------
<S>                                                                  <C>             <C>
OPERATING ACTIVITIES:
Net income (loss)                                                    $  2,742,693    $ (5,084,570)
Adjustments to reconcile net income (loss) to net cash provided by
 (used in) operating activities:
  Depreciation and amortization                                         1,495,201       1,559,845
  Amortization of intangible assets                                       752,376         752,376
  Noncash stock compensation                                              544,178         434,849
  Impairment charge and loss on disposal of equipment                     870,058          20,614
  Changes in operating assets and liabilities:
    Receivables                                                        (1,167,549)     (1,054,552)
    Inventories                                                          (528,742)        (28,486)
    Prepaid expenses and other assets                                    (137,050)        607,479
    Accounts payable                                                      697,651         239,201
    Accrued expenses and other liabilities                               (554,192)     (1,093,962)
    Deferred revenue                                                    5,575,576        (424,480)
                                                                     ------------    ------------
Net cash provided by (used in) operating activities                    10,290,200      (4,071,686)

INVESTING ACTIVITIES:
Purchases of equipment and leasehold improvements                        (206,934)       (119,367)
Proceeds on sale of equipment                                              58,020         290,551
Sales and maturities of short-term investments                                  0          48,000
                                                                     ------------    ------------
Net cash provided by (used in) investing activities                      (148,914)        219,184

FINANCING ACTIVITIES:
Proceeds of long-term debt                                                200,000               0
Payments on long-term debt                                                      0         (12,937)
Proceeds from common stock, net                                           840,580         383,579
                                                                     ------------    ------------
Net cash provided by financing activities                               1,040,580         370,642
                                                                     ------------    ------------
Net increase (decrease) in cash and cash equivalents                   11,181,866      (3,481,860)
Cash and cash equivalents at beginning of period                       47,015,746      49,301,501
                                                                     ------------    ------------
Cash and cash equivalents at end of period                           $ 58,197,612    $ 45,819,641
                                                                     ============    ============
</Table>

                 See accompanying notes to financialstatements.



                                       5
<PAGE>



                          THIRD WAVE TECHNOLOGIES, INC.

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  June 30, 2004
                                   (unaudited)

(1) Basis of Presentation

The accompanying unaudited consolidated financial statements of Third Wave
Technologies, Inc. have been prepared in accordance with accounting principles
generally accepted in the United States for interim financial information and
with the instructions to Form 10-Q and Article 10 of Regulation S-X.
Accordingly, they do not include all of the information and footnotes required
by accounting principles generally accepted in the United States for complete
financial statements. In the opinion of management, all adjustments, consisting
of normal recurring adjustments, considered necessary for a fair presentation
have been included. Interim results are not necessarily indicative of results
that may be expected for the year ending December 31, 2004.

The balance sheet at December 31, 2003 has been derived from the audited
financial statements at that date but does not include all of the information
and footnotes required by accounting principles generally accepted in the United
States for complete financial statements.

The accompanying unaudited consolidated financial statements should be read in
conjunction with the audited financial statements and footnotes thereto included
in our Form 10-K for the fiscal year ended December 31, 2003 filed with the
Securities and Exchange Commission.

(2) Net Income (Loss) Per Share

In accordance with accounting principles generally accepted in the United
States, basic net income (loss) per share has been computed using the
weighted-average number of shares of common stock outstanding during the
respective periods. Diluted net income (loss) per share takes into account the
weighted average shares from options that could potentially dilute basic net
income per share in the future. Shares associated with stock options are
excluded for the three months ended June 30, 2004 and the three and six months
ended June 30, 2003 because they are antidilutive for the periods.

The following table presents the calculation of basic and diluted net income
(loss) per share:

<Table>
<Caption>
                                                           THREE MONTHS ENDED JUNE 30,         SIX MONTHS ENDED JUNE 30,
                                                              2004              2003              2004             2003
                                                         --------------    --------------    --------------   --------------
<S>                                                      <C>               <C>               <C>              <C>
Numerator:

         Net income (loss)                               $     (105,730)   $   (2,160,745)   $    2,742,693   $   (5,084,570)

Denominator

         Weighted average shares outstanding - basic         40,325,351        39,699,313        40,201,932       39,631,630

         Dilutive securities - stock options                        N/A               N/A         1,672,876              N/A

         Weighted average shares outstanding - diluted       40,325,351        39,699,313        41,874,808       39,631,630

Basic net income (loss) per share                        $        (0.00)   $        (0.05)   $         0.07   $        (0.13)

Dilutive net income (loss) per share                     $        (0.00)   $        (0.05)   $         0.07   $        (0.13)
</Table>



                                       6
<PAGE>
(3) Stock-Based Compensation

    Third Wave has stock-based employee compensation plans. Statement of
Financial Accounting Standards (SFAS) No. 123, "Accounting for Stock-Based
Compensation", encourages, but does not require companies to record compensation
cost for stock-based employee compensation plans at fair value. We have chosen
to continue using the intrinsic value method prescribed in Accounting Principles
Board Opinion No. 25, "Accounting for Stock Issued to Employees", and related
interpretations, in accounting for our stock option plans.

    Had compensation cost been determined based upon the fair value at the grant
date for awards under the plans based on the provisions of SFAS No. 123, our
SFAS No. 123 pro forma net income (loss) and net income (loss) per share would
have been as follows:

<Table>
<Caption>
                                        THREE MONTHS ENDED JUNE 30,        SIX MONTHS ENDED JUNE 30,
                                           2004            2003             2004             2003
                                      -------------    -------------    -------------    -------------
<S>                                   <C>              <C>              <C>              <C>
Net income (loss), as reported        $    (105,730)   $  (2,160,745)   $   2,742,693    $  (5,084,570)
Add:  Stock based compensation,
   as reported                              311,617          199,576          544,178          434,849
Less: Stock-based compensation,
   using fair value method               (1,156,271)      (1,196,717)      (2,441,184)      (2,232,717)
                                      -------------    -------------    -------------    -------------

Pro forma net income (loss)           $    (950,384)   $  (3,157,886)   $     845,687    $  (6,882,438)
                                      =============    =============    =============    =============

Net income (loss) per share, basic,   $       (0.00)   $       (0.05)   $        0.07    $       (0.13)
as reported
Net income (loss) per share,          $       (0.00)   $       (0.05)   $        0.07    $       (0.13)
diluted, as reported
Pro forma net income (loss) per       $       (0.02)   $       (0.08)   $        0.02    $       (0.17)
share, basic
Pro forma net income (loss) per       $       (0.02)   $       (0.08)   $        0.02    $       (0.17)
share, diluted
</Table>

(4) Inventories

Inventories, consisting mostly of raw materials, are carried at the lower of
cost or market using the first-in, first-out (FIFO) method for determining cost.

Inventories consist of the following:

<Table>
<Caption>
                                                JUNE 30,       DECEMBER 31,
                                                 2004              2003
                                            --------------    --------------
<S>                                         <C>               <C>
Raw materials                               $    1,412,329    $    1,609,866
Finished goods and work in process               1,257,443           534,180
Reserve for excess and obsolete inventory         (746,984)         (750,000)
                                            --------------    --------------
Total inventories                           $    1,922,788    $    1,394,046
                                            ==============    ==============
</Table>

(5) Stock Compensation

Included in operating expenses are the following stock compensation charges, net
of reversals related to terminated employees:

<Table>
<Caption>
                                THREE MONTHS ENDED     SIX MONTHS ENDED
                                    JUNE 30,              JUNE 30,
                                 2004       2003       2004       2003
                               --------   --------   --------   --------
<S>                            <C>        <C>        <C>        <C>
Cost of goods sold             $  4,879   $ 14,369   $  9,961   $ 70,021
Research and development        272,610     11,370    350,945     24,142
Selling and marketing               485      2,636     68,486      5,856
General and administrative       33,643    171,201    114,786    334,830
                               --------   --------   --------   --------
    Total stock compensation   $311,617   $199,576   $544,178   $434,849
                               --------   --------   --------   --------
</Table>

                                       7
<PAGE>

(6) Comprehensive Income (Loss)

The components of comprehensive income (loss) are as follows:

<Table>
<Caption>
                                                   THREE MONTHS ENDED            SIX MONTHS ENDED
                                                         JUNE 30,                     JUNE 30,
                                                   2004           2003           2004          2003
                                               -----------    -----------    -----------   -----------
<S>                                            <C>            <C>            <C>           <C>
Net Income (Loss)                              $  (105,730)   $(2,160,745)   $ 2,742,693   $(5,084,570)
Other comprehensive loss:
    Foreign currency translation adjustments        (1,179)        (2,209)           171        (2,968)
                                               -----------    -----------    -----------   -----------
Comprehensive loss                             $  (106,909)   $(2,162,954)   $ 2,742,864   $(5,087,538)
                                               ===========    ===========    ===========   ===========
</Table>

(7) Derivative Instruments

We sell products in a number of countries throughout the world. In the quarters
ending June 30, 2004 and 2003, we sold certain products with the resulting
accounts receivable denominated in Japanese Yen. Simultaneous with such sales
and purchase order commitments, we purchased foreign currency forward contracts
to manage the risk associated with foreign currency collections in the normal
course of business. These derivative instruments have maturities of less than
one year and are intended to offset the effect of transaction gains and losses,
which arise when collections in a foreign currency are received after the asset
is generated. There were no contracts outstanding at June 30, 2004. The changes
in the fair value of the derivatives and the loss or gain on the hedged asset
relating to the risk being hedged are recorded currently in earnings.

(8) Amortizable Intangible Assets

    Amortizable intangible assets consist of the following:

<Table>
<Caption>
                                    JUNE 30, 2004                 DECEMBER 31, 2003
                              ----------------------------   ----------------------------
                                GROSS                          GROSS
                               CARRYING      ACCUMULATED      CARRYING      ACCUMULATED
                                AMOUNT       AMORTIZATION      AMOUNT       AMORTIZATION
                              -----------   --------------   -----------   --------------
<S>                           <C>           <C>              <C>           <C>
   Costs of settling patent
     Litigation               $10,533,248   $    5,634,500   $10,533,248   $    4,882,124
   Reacquired marketing and
     Distribution rights        2,211,111        2,211,111     2,211,111        2,211,111
   Customer agreements             38,000           38,000        38,000           38,000
                              -----------   --------------   -----------   --------------
             Total            $12,782,359   $    7,883,611   $12,782,359   $    7,131,235
                              ===========   ==============   ===========   ==============
</Table>

(9) Restructuring and Impairment of Long Lived Assets

During the third quarter of 2002, we announced a restructuring plan designed to
simplify product development and manufacturing operations and reduce operating
expenses. The restructuring charges recorded were determined based upon plans
submitted by the Company's management and approved by the Board of Directors
using information available at the time. The restructuring charge included $2.5
million for the consolidation of facilities, $500,000 for prepayment penalties
mainly under capital lease arrangements, an impairment charge of $7.2 million
for abandoned leasehold improvements and equipment to be sold and $900,000 of
other costs related to the restructuring. The Company also recorded a $1.1
million charge within cost of goods sold related to inventory that was
considered obsolete based upon the restructuring plan.

The facilities charge contained estimates based on the Company's potential to
sublease a portion of its corporate office. The Company has offered the
corporate office space for sublease, but has been unable to sublease the space.
Accordingly, the Company decreased its estimate of the amount of sublease income
it expects to receive. The estimated lease and operating expenses were also
reduced, based on a portion of the office space being utilized.

The following table shows the changes in the restructuring accrual since
December 31, 2003. The remaining restructuring balance of $1.3 million is for
rent payments on a non-cancelable lease, net of estimated sublease income, which
will continue to be paid over the lease term through 2011. The current portion
of the accrual is included in other accrued liabilities on the balance sheet and
the remainder is included in other long-term liabilities.


                                       8
<PAGE>

<Table>
<Caption>
<S>                                                  <C>
      Accrued restructuring balance at
        December 31, 2003                            $   1,414,044
      Payments made                                       (115,849)
                                                     -------------
      Accrued restructuring balance at
        June 30, 2004                                $   1,298,195
                                                     -------------
</Table>

(10)  Reclassifications

Certain reclassifications have been made to the 2003 financial statements to
conform to the 2004 presentation.

                          THIRD WAVE TECHNOLOGIES, INC.

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

This Management's Discussion and Analysis of Financial Condition and Results of
Operations as of June 30, 2004 and for the three and six months ended June 30,
2004 and 2003 should be read in conjunction with our Form 10-K for the fiscal
year ended December 31, 2003 filed with the Securities and Exchange Commission.
In this Form 10-Q, the terms "we," "us," "our," "Company," and "Third Wave" each
refer to Third Wave Technologies, Inc. The following discussion of our financial
condition and results of our operations should be read in conjunction with our
Financial Statements, including the Notes thereto, included elsewhere in this
Form 10-Q. This Form 10-Q contains forward-looking statements within the meaning
of Section 21E of the Securities Exchange Act of 1934, as amended, and Section
27A of the Securities Act of 1933, as amended. For a more detailed discussion of
such forward-looking statements and the potential risks and uncertainties that
may affect their accuracy, see the "Forward-Looking Statements" section of this
Form 10-Q.

OVERVIEW

Third Wave Technologies, Inc. is a leading molecular diagnostics company. We
believe our proprietary Invader(R) technology, a novel, chemistry-based
platform, is easier to use, more accurate and cost-effective, and enables higher
testing throughput than existing technology. These and other advantages
conferred by our technology platform are enabling us to provide physicians and
researchers with superior tools to diagnose and treat disease.

More than 110 clinical laboratory customers are using Third Wave's products. Our
customer base also includes the Japanese government's share of the International
Haplotype Map Project. Other customers include pharmaceutical and biotechnology
companies, academic research centers and major health care providers.

Third Wave markets a growing number of products including analyte-specific
reagents (ASRs). These ASRs allow certified clinical reference laboratories to
create assays to screen for cystic fibrosis and other inherited disorders, and
to test for the Factor V Leiden and a host of other mutations associated with
predisposition to cardiovascular and other diseases. The Company has developed
or plans to develop a menu of molecular diagnostic products for clinical
applications that include genetic testing, pharmacogenetics, chromosomal
analysis, infectious disease, and women's health. The Company also has a number
of other Invader(R) products including those for research, agricultural and
other applications.

Our financial results may vary significantly from quarter to quarter due to
fluctuations in the demand for our products, timing of new product introductions
and deliveries made during the quarter, the timing of research, development and
grant revenues, and increases in spending, including expenses related to our
product development.

CRITICAL ACCOUNTING POLICIES

    Management's discussion and analysis of our financial condition and results
of operations are based upon our consolidated financial statements, which have
been prepared in accordance with accounting principles generally accepted in the
United States. We review the accounting policies we use in reporting our
financial results on a regular basis. The preparation of these financial
statements requires us to make estimates and judgments that affect the reported
amounts of assets, liabilities, revenues and expenses and related disclosure of
contingent assets and liabilities. On an ongoing basis, we evaluate our
estimates, including those related to accounts receivable, inventories,
equipment and leasehold improvements and intangible assets. We base our
estimates on historical



                                       9
<PAGE>

experience and on various other assumptions that are believed to be reasonable
under the circumstances, the results of which form the basis for making
judgments about the carrying value of assets and liabilities that are not
readily apparent from other sources. Results may differ from these estimates due
to actual outcomes being different from those on which we based our assumptions.
These estimates and judgments are reviewed by management on an ongoing basis,
and by the Audit Committee at the end of each quarter prior to the public
release of our financial results. We believe the following critical accounting
policies affect our more significant judgments and estimates used in the
preparation of our consolidated financial statements.

RESTRUCTURING AND OTHER CHARGES.

    The restructuring and other charges resulting from the restructuring plan in
the third quarter of 2002 has been recorded in accordance with EITF Issue No.
94-3, "Liability Recognition for Certain Employee Termination Benefits and Other
Costs to Exit an Activity (including Certain Costs Incurred in a
Restructuring)", Staff Accounting Bulletin No. 100, "Restructuring and
Impairment Charges," and Statement of Financial Accounting Standards (SFAS) No.
144, "Accounting for the Impairment or Disposal of Long-Lived Assets." The
restructuring charge was comprised primarily of costs to consolidate facilities,
impairment charges for abandoned leasehold improvements and equipment to be sold
or abandoned, prepayment penalties related mainly to capital lease obligations
on equipment to be sold or abandoned, and other costs related to the
restructuring. The remaining accrued restructuring balance is for rent payments
on a non-cancelable lease, net of estimated sublease income. In calculating the
cost to consolidate the facilities, we estimated the future lease and operating
costs to be paid until the leases are terminated and the amount, if any, of
sublease receipts for each location. This required us to estimate the timing and
costs of each lease to be terminated, the amount of operating costs, and the
timing and rate at which we might be able to sublease the site. To form our
estimates for these costs, we performed an assessment of the affected facilities
and considered the current market conditions for each site. Our assumptions on
the lease termination payments, operating costs until terminated, and the
offsetting sublease receipts may turn out to be incorrect and our actual cost
may be materially different from our estimates.

LONG-LIVED ASSETS--IMPAIRMENT

    Equipment, leasehold improvements and amortizable identifiable intangible
assets are reviewed for impairment whenever events or changes in circumstances
indicate that the carrying amount may not be recoverable. For assets held and
used, if the sum of the expected undiscounted cash flows is less than the
carrying value of the related asset or group of assets, a loss is recognized for
the difference between the fair value and carrying value of the asset or group
of assets. For assets removed from service and held for sale, we estimate the
fair market value of such assets and record an adjustment if fair value less
costs to sell is lower than carrying value. In the quarter ended June 30, 2004
we recorded an impairment charge of $0.8 million on certain equipment.

    Goodwill and intangible assets deemed to have indefinite lives are not
amortized, but are subject to annual impairment tests under SFAS No. 142,
"Goodwill and Other Intangible Assets." The annual impairment tests are
completed in the quarter ended September 30. An impairment test was performed in
the quarter ended June 30, 2004 due to a change in our forecast. Based on the
analysis, it was determined that there was no impairment of goodwill or
intangible assets with indefinite lives.

DERIVATIVE INSTRUMENTS

    We sell products in a number of countries throughout the world. During 2004
and 2003, we sold certain products with the resulting accounts receivable
denominated in Japanese Yen. Simultaneous with such sales and purchase order
commitments, we purchased foreign currency forward contracts to manage the risk
associated with collections of receivables denominated in foreign currencies in
the normal course of business. These derivative instruments have maturities of
less than one year and are intended to offset the effect of transaction gains
and losses. There were no contracts outstanding at June 30, 2004. The changes in
the fair value of the derivatives and the loss or gain on the hedged asset
relating to the risk being hedged are recorded currently in earnings.

INVENTORIES--SLOW MOVING AND OBSOLESCENCE

    Significant management judgment is required to determine the reserve for
obsolete or excess inventory. Inventory on hand may exceed future demand either
because of process improvements or technology advancements, the amount on hand
is more than can be used to meet future need, or estimates of shelf lives may
change. We currently consider all inventory that we expect will have no activity
within one year as well as any additional specifically identified inventory to
be subject to a provision for excess inventory. We also provide for the total
value of inventories that we determine to be obsolete based on criteria such as
changing manufacturing processes and technologies. At June 30, 2004, our
inventory reserves were $0.7 million, or 28% of our $2.7 million total gross
inventories. As of June 30, 2004, 27% of our gross inventory was held at a
customer site pending inspection for approval.



                                       10
<PAGE>

RESULTS OF OPERATIONS

Three and Six Months Ended June 30, 2004 and 2003

REVENUES. Revenues for the three months ended June 30, 2004 of $12.6 million
represented an increase of $3.8 million, compared to revenues of $8.8 million
for the corresponding period of 2003. Revenues for the six months ended June 30,
2004 of $27.9 million represented an increase of $10.6 million, compared to
revenues of $17.3 million for the corresponding period of 2003.

Product revenues increased to $12.5 million for the quarter ended June 30, 2004,
from $8.5 million in the quarter ended June 30, 2003. Product revenues increased
to $27.8 million for the six months ended June 30, 2004, from $16.7 million in
the six months ended June 30, 2003. The increase in product sales during the
three and six months ending June 30, 2004 was due to an increase in sales of
genomic research product to a major Japanese research institute and an increase
in molecular diagnostic sales compared to the corresponding periods of 2003. We
expect our molecular diagnostic revenues to increase throughout 2004.

We had no development revenues for the three months ended June 30, 2004,
compared to development revenues of $0.3 million for the three months ended June
30, 2003. We had no development revenues for the six months ended June 30, 2004,
compared to development revenues of $0.5 million for the six months ended June
30, 2003. The decrease was due to the transition from development revenue to
product revenue in our development and commercialization agreement with BML,
Inc.

Significant Customer. We generated $19.1 million, or 68% of our revenues, from
sales to a major Japanese research institute for use by several end-users during
the six months ended June 30, 2004. As of June 30, 2004, $0.7 million of our
accounts receivable were attributable to this customer. We also recorded
deferred revenue of $5.1 million related to a product shipment that is subject
to acceptance by this customer. This customer will continue to purchase Company
products in 2004, however, the timing and total of such purchases will be
influenced by the Japanese government funding process and amounts which are
unpredictable and unknown to Third Wave.

COST OF GOODS SOLD. Cost of goods sold consists of materials used in the
manufacture of product, depreciation on manufacturing capital equipment,
salaries and related expenses for management and personnel associated with our
manufacturing and quality control departments and amortization of licenses and
settlement fees. For the three months ended June 30, 2004, cost of goods sold
increased to $3.5 million, compared to $3.4 million for the corresponding period
of 2003. For the six months ended June 30, 2004, cost of goods sold increased to
$7.6 million, compared to $6.5 million for the corresponding period of 2003. The
increase was primarily due to the increase in sales volume. We expect gross
margin to improve as molecular diagnostic revenues increase.

RESEARCH AND DEVELOPMENT EXPENSES. Research and development expenses consist
primarily of salaries and related personnel costs, material costs for assays and
product development, fees paid to consultants, depreciation and facilities costs
and other expenses related to the design, development, testing and enhancement
of our products and acquisition of technologies used or to be used in our
products. Research and development costs are expensed as they are incurred.
Research and development expenses for the three months ended June 30, 2004 were
$3.4 million, compared to $2.9 million for the three months ended June 30, 2003.
Research and development expenses for the six months ended June 30, 2004 were
$6.3 million, compared to $5.8 million for the six months ended June 30, 2003.
The increase in research and development expenses was primarily due to an
increase in personnel related expenses. We will continue to invest in research
and development, and expenditures in this area may increase as we expand our
product development efforts.

SELLING AND MARKETING EXPENSES. Selling and marketing expenses consist primarily
of salaries and related personnel costs for our sales and marketing management
and field sales force, commissions, office support and related costs, and travel
and entertainment. Selling and marketing expenses for the three months ended
June 30, 2004 were $2.7 million, an increase of $0.2 million, compared to $2.5
million for the corresponding period of 2003. Selling and marketing expenses for
the six months ended June 30, 2004 were $5.3 million, an increase of $0.4
million, compared to $4.9 million for the corresponding period of 2003. The
increase in the six months ended June 30, 2004 was due to an increase in
personnel related expenses compared to the same period in 2003. We anticipate
selling and marketing expenses to continue to be at or above 2003 levels.

GENERAL AND ADMINISTRATIVE EXPENSES. General and administrative expenses consist
primarily of salaries and related expenses for executive, finance and other
administrative personnel, legal and professional fees, office support and
depreciation. General and administrative expenses increased to $3.1 million in
the three months ended June 30, 2004, from $2.2 million for the corresponding
period in 2003. General and administrative expenses decreased to $5.3 million in
the six months ended June 30, 2004,



                                       11
<PAGE>

from $5.4 million for the corresponding period in 2003. The increase in the
three months ended June 30, 2004 was due to an increase in personnel related
expenses compared to the corresponding period of 2003.

IMPAIRMENT CHARGE. In the three months ended June 30, 2004 an impairment charge
of $0.8 million was recorded for equipment written down to fair value.

INTEREST INCOME. Interest income for the three months ended June 30, 2004 was
$0.1 million, compared to $0.2 million for the corresponding period of 2003.
Interest income for the six months ended June 30, 2004 and 2003 was $0.3
million.

INTEREST EXPENSE. Interest expense for the three months ended June 30, 2004 and
2003 was approximately $0.1 million. Interest expense for the six months ended
June 30, 2004 was $0.1 million compared to $0.2 million for the six months ended
June 30, 2003.

OTHER INCOME (EXPENSE): Other income for the three months ended June 30, 2004
was $0.6 million, compared to other income of $8,000 for the three months ended
June 30, 2003. Other expense for the three months ended June 30, 2004 was $0.1
million, compared to other income of $34,000 for the six months ended June 30,
2003. The increase in other income was due to the adjustment of foreign currency
contracts.

LIQUIDITY AND CAPITAL RESOURCES

Since our inception, we have financed our operations primarily through private
placements of equity securities, research grants from federal and state
government agencies, payments from strategic collaborators, equipment loans,
capital leases, sale of products, a convertible note and an initial public
offering. As of June 30, 2004, we had cash and cash equivalents and short-term
investments of $69.0 million.

Net cash provided by operations for the six months ended June 30, 2004 was $10.3
million, compared to net cash used in operations of $4.1 million in the
corresponding period in 2003. The increase in cash provided by operations was
primarily due to the increase in revenue and deferred revenue.

    Net cash used in investing activities for the six months ended June 30, 2004
was $0.1 million, compared to net cash provided by investing of $0.2 million in
the corresponding period in 2003. Investing activities included capital
expenditures of $0.2 million in the six months ended June 30, 2004, compared to
$0.1 million in the corresponding period in 2003. Investing activities included
proceeds from the sale of equipment of $0.1 million in the six months ended June
30, 2004, compared to $0.3 million in the corresponding period in 2003.
Investing activities in the six months ended June 30, 2003 also included $48,000
from the maturity of short-term investments.

    Net cash provided by financing activities was $1.0 million in the six months
ended June 30, 2004, compared to $0.4 million in the six months ended June 30,
2003. Cash provided by financing activities in the six months ending June 30,
2004 consisted of proceeds from the sale of common stock of $0.8 million
compared to $0.4 million in the corresponding period of 2003. In the six months
ended June 30, 2004, there was $0.2 million of proceeds from long-term debt. In
the six months ended June 30, 2003, $13,000 was used to repay debt.

    The following summarizes our contractual obligations at June 30, 2004 and
the effect those obligations are expected to have on our liquidity and cash flow
in future periods (in thousands):

<Table>
<Caption>
                                             TOTAL   LESS THAN    YEARS     YEARS     OVER
                                                        1 YEAR    2 - 3     4 - 5    5 YEARS
                                             ------- ---------   -------   -------   -------
<S>                                          <C>     <C>         <C>       <C>       <C>
CONTRACTUAL OBLIGATION
Non-cancelable operating lease obligations   $14,505 $   1,711   $ 3,759   $ 4,066   $ 4,969
Term loan                                      9,713     9,558       155        --        --
                                             ------- ---------   -------   -------   -------
Total obligation                             $24,218 $  11,269   $ 3,914   $ 4,066   $ 4,969
                                             ------- ---------   -------   -------   -------
</Table>

As of December 31, 2003 and June 30, 2004, a valuation allowance equal to 100%
of our net deferred tax assets had been recognized since our future realization
is not assured. At December 31, 2003, we had federal and state net operating
loss carryforwards of approximately $114 million. The net operating loss
carryforwards will expire at various dates beginning in 2008, if not utilized.
Utilization of the net operating losses and credits to offset future taxable
income may be subject to an annual limitation due to the



                                       12
<PAGE>

change of ownership provisions of federal tax laws and similar state provisions
as a result of the initial public offering in February 2001.

We cannot assure you that our business or operations will not change in a manner
that would consume available resources more rapidly than anticipated. We also
cannot assure you that we will not require substantial additional funding before
we can achieve profitable operations. Our capital requirements depend on
numerous factors, including the following:

    o   our progress with our research and development programs;

    o   our level of success in selling our products and technologies;

    o   our ability to establish and maintain successful collaborative
        relationships;

    o   the costs we incur in enforcing and defending our patent claims and
        other intellectual property rights; and

    o   the timing of purchases of additional capital.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Our exposure to market risk is currently confined to changes in foreign exchange
and interest rates. The securities in our investment portfolio are not leveraged
and, due to their short-term nature, are subject to minimal interest rate risk.
We currently do not hedge interest rate exposure. Due to the short-term
maturities of our investments, we do not believe that an increase in market
rates would have any negative impact on the realized value of our investment
portfolio.

To reduce foreign exchange risk, we selectively use financial instruments. Our
earnings are affected by fluctuations in the value of the U.S. dollar against
foreign currencies as a result of the sales of our products in foreign markets.
Forward foreign exchange contracts are used to hedge against the effects of such
fluctuations. Our policy prohibits the trading of financial instruments for
profit. A discussion of our accounting policies for derivative financial
instruments is included in the notes to the financial statements.

ITEM 4. CONTROLS AND PROCEDURES

As required by Rule 13a-15(b) under the Securities Exchange Act of 1934, the
Company's management, including the Company's Chief Executive Officer and Chief
Financial Officer, conducted an evaluation as of the end of the period covered
by this report, of the effectiveness of the Company's disclosure controls and
procedures as defined in Rule 13a-15(e) under the Securities Exchange Act of
1934. Based on that evaluation, the Company's Chief Executive Officer and Chief
Financial Officer concluded that the Company's disclosure controls and
procedures were effective as of the end of the period covered by this report. As
required by Rule 13a-15(d) under the Securities Exchange Act of 1934 the
Company's management, including the Company's Chief Executive Officer and Chief
Financial Officer, also conducted an evaluation of the company's internal
control over financial reporting to determine whether any changes occurred
during the quarter covered by this report that have materially affected, or are
reasonably likely to materially affect, the Company's internal control over
financial reporting. Based on that evaluation, there has been no such change
during the quarter covered by this report.

FORWARD-LOOKING STATEMENTS

This Form 10-Q contains forward-looking statements within the meaning of Section
21E of the Securities Exchange Act of 1934, as amended, and Section 27A of the
Securities Act of 1933, as amended. When used in this Form 10-Q the words
"believe," "anticipates," "intends," "plans," "estimates," and similar
expressions are forward-looking statements. Such forward-looking statements
contained in this Form 10-Q are based on current expectations. Forward-looking
statements may address the following subjects: results of operations; customer
growth and retention; development of technologies; losses or earnings; operating
expenses, including, without limitation, marketing expense and technology and
development expense; and revenue growth. We caution investors that there can be
no assurance that actual results, outcomes or business conditions will not
differ materially from those projected or suggested in such forward-looking
statements as a result of various factors, including, among others, our limited
operating history, unpredictability of future revenues and operating results,
competitive pressures and also the potential risks and uncertainties set forth
in the "Overview" section hereof and in the "Overview" and "Risk Factors"
sections of our annual report on Form 10-K for the fiscal year ended December
31, 2003 filed with the Securities and Exchange Commission, which factors are
specifically incorporated herein by this reference. You should also carefully
consider the factors set forth in other reports or documents that we file from
time to time



                                       13
<PAGE>

with the Securities and Exchange Commission. Except as required by law, we
undertake no obligation to update any forward-looking statements.

                          PART II - OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS - There are no material legal proceedings pending.
    From time to time, we may be involved in litigation relating to claims
    arising out of our operations in the usual course of business.

ITEM 2. CHANGES IN SECURITIES, USE OF PROCEEDS, AND ISSUER PURCHASES OF EQUITY
        SECURITIES.

    (a) None

    (b) None

    (c) None

    (d) Use of Proceeds. Pursuant to our Registration Statement on Form S-1, as
        amended, filed with the Securities and Exchange Commission and declared
        effective February 9, 2001, (Registration No. 333-42694), we commenced
        our initial public offering of 7,500,000 registered shares of common
        stock, $0.001 par value, on February 9, 2001, at a price of $11.00 per
        share (the "Offering"). The Offering was completed on February 14, 2001,
        and all of the 7,500,000 shares were sold, generating gross proceeds of
        approximately $82,500,000. The managing underwriters for the Offering
        were Lehman Brothers Inc., CIBC World Markets, Dain Rauscher
        Incorporated, Robert W. Baird & Co. Incorporated, and Fidelity Capital
        Markets.

        In connection with the Offering, we incurred approximately $5.8 million
        in underwriting discounts and commissions, and approximately $1.9
        million in other related expenses. The net offering proceeds to us,
        after deducting the foregoing expenses, were approximately $74.8
        million.

        From the time of receipt through June 30, 2004, we have invested the net
        proceeds from the Offering in investment-grade, interest-bearing
        securities. We used $4.0 million of the proceeds to satisfy a
        cancellation fee for the termination of a distribution agreement with
        Endogen Corporation. We used approximately $14.0 million for general
        corporate purposes, including working capital and research and
        development activities.

        We expect to use the remainder of the net proceeds for general corporate
        purposes, including working capital and expanding research and
        development and sales and marketing efforts to accelerate the
        commercialization of new products and the development of new
        partnerships.

        A portion of the net proceeds may also be used to acquire or invest in
        complementary businesses or products to obtain the right to use
        complementary technologies. From time to time, in the ordinary course of
        business, we may evaluate potential acquisitions of these businesses,
        products, or technologies. We have no current agreements or commitments
        regarding any such transaction.

    (e) None

ITEM 3. DEFAULTS UPON SENIOR SECURITIES - None.

ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS:

         At the Annual Meeting of Shareholders held on June 22, 2004, the
    following matters were submitted to a vote of security holders:

    (a)  Three directors were elected for terms of three years each, as follows:

<Table>
<Caption>
Director                   Votes FOR            Votes WITHHELD
<S>                        <C>                    <C>
Lance Fors                 32,715,869             3,611,696
David Thompson             33,546,753             2,780,812
John J. Puisis             35,992,677               334,888
</Table>

    (b) The appointment of Ernst & Young LLP as the Company's independent
        auditors for the fiscal year ending December 31, 2004 was ratified, as
        follows:


                                       14
<PAGE>
<Table>
<Caption>
     Votes FOR          Votes AGAINST        Votes ABSTAIN      Broker NON-VOTES
<S>                     <C>                  <C>                <C>
     35,926,229           395,932                5,404                 0
</Table>

ITEM 5. OTHER INFORMATION - None.

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

    (a) Exhibits.

     10.1 Amendment No. 1 to Employment Agreement between Lance Fors and Third
          Wave Technologies, Inc. dated June 14, 2004

     10.2 Amendment No. 2 to Employment Agreement between John Puisis and Third
          Wave Technologies, Inc. dated June 14, 2004

     31.1 Rule 13a-14(a)/15d-14(a) Certification of Chief Executive Officer

     31.2 Rule 13a-14(a)/15d-14(a) Certification of Chief Financial Officer

     32   Section 1350 Certifications

     (b)  Reports on Form 8-K filed during the three months ended June 30, 2004:
          The Company filed a Form 8-K dated April 28, 2004 reporting the
          Company's press releases dated April 28, 2004 announcing the Company's
          quarter ending March 31, 2004 financial results. The Company filed a
          Form 8-K dated May 6, 2004 reporting the Company's press releases
          dated May 6, 2004 announcing the Company's management succession plan.

                                       15
<PAGE>

                                   SIGNATURES

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.

                                                 THIRD WAVE TECHNOLOGIES, INC.

        Date: August 9, 2004                        /s/ John Puisis
                                                    ----------------------------
                                                    John Puisis, CEO

        Date: August 9, 2004                        /s/ David Nuti
                                                    ----------------------------
                                                    David Nuti, CFO