<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, 2005 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 August 5, 2005, was 41,059,769.


<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.
                          QUARTERLY REPORT ON FORM 10-Q
                       FOR THE QUARTER ENDED JUNE 30, 2005

                                TABLE OF CONTENTS


<Table>
<Caption>
                                                                                                                PAGE NO.
<S>                                                                                                             <C>
PART I FINANCIAL INFORMATION....................................................................................   3
    Item 1. Consolidated Financial Statements...................................................................   3
       Consolidated Balance Sheets as of June 30, 2005 and December 31, 2004....................................   3
       Consolidated Statements of Operations for the three and six months ended June 30, 2005 and 2004..........   4
       Consolidated Statements of Cash Flows for the six months ended June 30, 2005 and 2004....................   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..........................................  12
    Item 4. Controls and Procedures.............................................................................  13
PART II OTHER INFORMATION.......................................................................................  13
    Item 1. Legal Proceedings...................................................................................  13
    Item 2. Unregistered Sales of Equity Securities and Use of Proceeds.........................................  13
    Item 3. Defaults Upon Senior Securities.....................................................................  14
    Item 4. Submission Of Matters To A Vote Of Security Holders.................................................  14
    Item 5. Other Information...................................................................................  14
    Item 6. Exhibits............................................................................................  14
SIGNATURES......................................................................................................  15
EXHIBITS........................................................................................................  16
</Table>



                                       2
<PAGE>

                         PART I - FINANCIAL INFORMATION
                          ITEM 1. FINANCIAL STATEMENTS
                          THIRD WAVE TECHNOLOGIES, INC.
                           Consolidated Balance Sheets

<Table>
<Caption>
                                                                                    JUNE 30, 2005         DECEMBER 31, 2004
                                                                                      UNAUDITED
<S>                                                                                 <C>                   <C>
ASSETS
Current assets:
  Cash and cash equivalents                                                         $  49,623,201           $  55,619,981
  Short-term investments                                                               11,870,000              11,070,000
  Receivables, net of allowance for doubtful accounts of $185,000
    and $300,000, respectively                                                          3,886,675               5,784,679
  Inventories                                                                           2,066,933               1,236,392
  Prepaid expenses and other                                                              495,014                 260,316
                                                                                    -------------           -------------
Total current assets                                                                   67,941,823              73,971,368
Equipment and leasehold improvements:
  Machinery and equipment                                                              15,534,371              15,832,489
  Leasehold improvements                                                                2,290,787               2,277,604
                                                                                    -------------           -------------
                                                                                       17,825,158              18,110,093
  Less accumulated depreciation                                                        12,573,820              12,139,423
                                                                                    -------------           -------------
                                                                                        5,251,338               5,970,670
                                                                                    -------------           -------------
Assets held for sale                                                                            0                 269,000
Intangible assets, net of accumulated amortization                                      3,393,996               4,146,372
Indefinite lived intangible assets                                                      1,007,411               1,007,411
Goodwill                                                                                  489,873                 489,873
Other long term assets                                                                  1,923,598               2,212,935
                                                                                    -------------           -------------
Total assets                                                                        $  80,008,039           $  88,067,629
                                                                                    =============           =============

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities:
  Accounts payable                                                                  $   8,712,554           $   6,519,005
  Accrued payroll and related liabilities                                               1,914,428               2,873,506
  Other accrued liabilities                                                             2,087,378               1,867,361
  Deferred revenue                                                                        279,799                 129,530
  Capital lease obligations                                                                99,353                  66,867
  Long-term debt due within one year                                                    9,848,272               9,614,127
                                                                                    -------------           -------------
Total current liabilities                                                              22,941,784              21,070,396
Long-term debt                                                                            844,502                 335,069
Deferred revenue - long term                                                              199,908                 254,434
 Capital lease obligations - long term                                                    226,215                 151,885
Other liabilities                                                                       4,295,266               3,520,948
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, 41,232,519
    issued, 41,014,519 outstanding at June 30, 2005 and 41,102,764 shares
    issued and outstanding at December 31, 2004                                            41,233                  41,103
  Additional paid-in capital                                                          198,435,910             198,990,162
  Unearned stock compensation                                                            (427,638)               (554,293)
  Treasury stock, 218,000 shares were acquired at an average of
    $4.02 per share                                                                      (877,159)                      -
  Foreign currency translation adjustment                                                  36,511                  31,949
  Accumulated deficit                                                                (145,708,493)           (135,774,024)
                                                                                    -------------           -------------
Total shareholders' equity                                                             51,500,364              62,734,897
                                                                                    -------------           -------------
Total liabilities and shareholders' equity                                          $  80,008,039           $  88,067,629
                                                                                    =============           =============
</Table>



          See accompanying notes to consolidated 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,
                                                          --------------------------------        --------------------------------
                                                              2005                2004                2005                2004
                                                          ------------        ------------        ------------        ------------
<S>                                                       <C>                 <C>                 <C>                 <C>
Revenues:
     Product sales                                        $  5,574,109        $ 12,528,877        $ 12,488,385        $ 27,743,515
     License and royalty revenue                                89,763              54,988             182,846              95,629
     Grant revenue                                             107,642              48,402             226,526              68,732
                                                          ------------        ------------        ------------        ------------
Total revenues                                               5,771,514          12,632,267          12,897,757          27,907,876
                                                          ------------        ------------        ------------        ------------
Operating expenses:
     Cost of goods sold
        Product cost of goods sold                           1,313,230           3,152,096           2,851,909           6,751,856
        Intangible and long term asset amortization            498,194             541,561             959,590           1,112,657
                                                          ------------        ------------        ------------        ------------
     Total cost of goods sold                                1,811,424           3,693,657           3,811,499           7,864,513

     Research and development                                2,040,159           3,027,310           4,505,538           5,700,186
     Selling and marketing                                   3,181,569           2,696,218           6,546,063           5,320,991
     General and administrative                              4,267,698           3,212,214           8,046,959           5,569,605
     Impairment charge                                         202,707             758,716             202,707             758,716
                                                          ------------        ------------        ------------        ------------
Total operating expenses                                    11,503,557          13,388,115          23,112,766          25,214,011
                                                          ------------        ------------        ------------        ------------
Income (loss) from operations                               (5,732,043)           (755,848)        (10,215,009)          2,693,865
Other income (expense):
     Interest income                                           393,338             142,758             740,338             269,948
     Interest expense                                          (95,376)            (58,755)           (184,762)           (115,749)
     Other                                                     (79,849)            566,115            (275,036)           (105,371)
                                                          ------------        ------------        ------------        ------------
Other income                                                   218,113             650,118             280,540              48,828
                                                          ------------        ------------        ------------        ------------
Net income (loss)                                         $ (5,513,930)       $   (105,730)       $ (9,934,469)       $  2,742,693
                                                          ============        ============        ============        ============

Net income (loss) per share - basic                       $      (0.13)       $      (0.00)       $      (0.24)       $       0.07
                                                          ============        ============        ============        ============
Net income (loss) per share - diluted                     $      (0.13)       $      (0.00)       $      (0.24)       $       0.07
                                                          ============        ============        ============        ============
Weighted average shares outstanding
       Basic                                                41,087,554          40,325,351          41,105,285          40,201,932
                                                          ============        ============        ============        ============
       Diluted                                              41,087,554          40,325,351          41,105,285          41,874,808
                                                          ============        ============        ============        ============
</Table>


          See accompanying notes to consolidated financial statements.



                                       4
<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.

                      Consolidated Statements of Cash Flows
                                   (Unaudited)

<Table>
<Caption>
                                                                                          SIX MONTHS ENDED
                                                                                               JUNE 30,
                                                                                   --------------------------------
                                                                                       2005                2004
                                                                                   ------------        ------------
<S>                                                                                <C>                 <C>
OPERATING ACTIVITIES:
Net income (loss)                                                                  $ (9,934,469)       $  2,742,693
Adjustments to reconcile net income (loss) to net cash provided by (used in)
  operating activities:
   Depreciation and amortization                                                      1,089,694           1,495,201
   Amortization of intangible assets                                                    752,376             752,376
   Noncash stock compensation                                                          (777,184)            544,178
    Impairment charge and loss on disposal of equipment                                 211,403             870,058
   Changes in operating assets and liabilities:
     Receivables                                                                      1,902,566          (1,167,549)
     Inventories                                                                       (830,541)           (528,742)
     Prepaid expenses and other assets                                                 (152,575)           (137,050)
     Accounts payable                                                                 2,193,549             697,651
     Accrued expenses and other liabilities                                              35,257            (554,192)
     Deferred revenue                                                                    95,743           5,575,576
                                                                                   ------------        ------------
Net cash provided by (used in) operating activities                                  (5,414,181)         10,290,200

INVESTING ACTIVITIES:
Purchases of equipment and leasehold improvements                                      (150,436)           (206,934)
Proceeds on sale of equipment                                                           193,231              58,020
Purchases of short-term investments                                                    (800,000)                  0
                                                                                   ------------        ------------
Net cash used in investing activities                                                  (757,205)           (148,914)

FINANCING ACTIVITIES:
Proceeds of long-term debt                                                              800,000             200,000
Payments on long-term debt                                                              (56,422)                  0
Payment on capital lease obligations                                                    (41,530)                  0
Proceeds from issuance of common stock, net                                             349,717             840,580
Repurchase of stock                                                                    (877,159)                  0
                                                                                   ------------        ------------
Net cash provided by financing activities                                               174,606           1,040,580
                                                                                   ------------        ------------
Net increase (decrease) in cash and cash equivalents                                 (5,996,780)         11,181,866
Cash and cash equivalents at beginning of period                                     55,619,981          47,015,746
                                                                                   ------------        ------------
Cash and cash equivalents at end of period                                         $ 49,623,201        $ 58,197,612
                                                                                   ============        ============
</Table>

During the six months ended June 30, 2005, the Company entered into capital
lease obligations of $148,346.


          See accompanying notes to consolidated financial statements.


                                       5
<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  June 30, 2005
                                   (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, 2005.

The balance sheet at December 31, 2004 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, 2004 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 and six months ended June 30, 2005 and three months ended
June 30, 2004 because they are anti-dilutive.

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,
                                                               2005                2004                 2005                2004
                                                               ----                ----                 ----                ----
<S>                                                        <C>                 <C>                 <C>                 <C>
Numerator:
       Net income (loss)                                   $ (5,513,930)       $   (105,730)       $ (9,934,469)       $  2,742,693
Denominator
       Weighted average shares outstanding - basic           41,087,554          40,325,351          41,105,285          40,201,932
       Dilutive securities - stock options                          N/A                 N/A                 N/A           1,672,876
       Weighted average shares outstanding - diluted         41,087,554          40,325,351          41,105,285          41,874,808
Basic net income (loss) per share                          $      (0.13)       $      (0.00)       $      (0.24)       $       0.07
Dilutive net income (loss) per share                       $      (0.13)       $      (0.00)       $      (0.24)       $       0.07
</Table>

(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:


                                       6
<PAGE>


<Table>
<Caption>
                                                                     THREE MONTHS ENDED JUNE 30,       SIX MONTHS ENDED JUNE 30,
                                                                        2005             2004             2005              2004
                                                                        ----             ----             ----              ----
<S>                                                                <C>              <C>              <C>              <C>
Net income (loss), as reported                                     $ (5,513,930)    $   (105,730)    $ (9,934,469)    $  2,742,693
  Add: Stock-based compensation, as reported                           (362,720)         311,617         (777,184)         544,178
  Less: Stock-based compensation, using fair value method            (1,275,716)      (1,145,183)      (2,339,730)      (2,199,126)
  Less: Stock-based compensation, related to the employee stock
  purchase plan determined under SFAS No. 123                           (95,847)        (151,017)         (95,847)        (151,017)
                                                                   ------------     ------------     ------------     ------------
Pro forma net income (loss)                                        $ (7,248,213)    $ (1,090,313)    $(13,147,230)    $    936,728
                                                                   ============     ============     ============     ============
Net income (loss) per share, basic, as reported                    $      (0.13)    $      (0.00)    $      (0.24)    $       0.07
Net income (loss) per share, diluted, as reported                  $      (0.13)    $      (0.00)    $      (0.24)    $       0.07
Pro forma net income (loss) per share, basic                       $      (0.18)    $      (0.03)    $      (0.32)    $       0.02
Pro forma net income (loss) per share, diluted                     $      (0.18)    $      (0.03)    $      (0.32)    $       0.02
</Table>

        As described in Note 2 of Notes to Consolidated Financial Statements in
our Form 10-K for the year ended December 31, 2004, the Financial Accounting
Standards Board recently issued SFAS No. 123 (revised 2004), "Share-Based
Payment", which is a revision of SFAS No. 123. The Company expects to adopt SFAS
No. 123(R) on January 1, 2006.

(4) Inventories

Inventories 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,
                                                       2005                  2004
                                                   -----------           -----------
<S>                                                <C>                   <C>
Raw materials                                      $ 1,616,185           $ 1,318,771
Finished goods and work in process                   1,135,748               567,621
Reserve for excess and obsolete inventory             (685,000)             (650,000)
                                                   -----------           -----------
Total inventories                                  $ 2,066,933           $ 1,236,392
                                                   ===========           ===========
</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,
                                        2005                2004               2005                2004
                                        ----                ----               ----                ----
<S>                                  <C>                 <C>                <C>                 <C>
Cost of goods sold                   $  (7,231)          $   4,879          $ (12,980)          $   9,961
Research and development              (241,232)            272,610           (501,082)            350,945
Selling and marketing                  (17,301)                485             12,407              68,486
General and administrative             (96,956)             33,643           (275,529)            114,786
                                     ---------           ---------          ---------           ---------
   Total stock compensation          $(362,720)          $ 311,617          $(777,184)          $ 544,178
                                     ---------           ---------          ---------           ---------
</Table>

(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,
                                                         2005                  2004                  2005                  2004
                                                         ----                  ----                  ----                  ----
<S>                                                  <C>                   <C>                   <C>                   <C>
Net income (loss)                                    $(5,513,930)          $  (105,730)          $(9,934,469)          $ 2,742,693
Other comprehensive income (loss):
   Foreign currency translation adjustments                5,416                (1,179)                4,562                   171
                                                     -----------           -----------           -----------           -----------
Comprehensive income (loss)                          $(5,508,514)          $  (106,909)          $(9,929,907)          $ 2,742,864
                                                     ===========           ===========           ===========           ===========
</Table>



                                       7
<PAGE>

(7) Derivative Instruments

We sell products in a number of countries throughout the world. In the quarters
ended June 30, 2005 and 2004, 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, 2005. 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 in earnings.

(8) Amortizable Intangible Assets

Amortizable intangible assets consist of the following:

<Table>
<Caption>
                                                                 JUNE 30, 2005                         DECEMBER 31, 2004
                                                      ---------------------------------------------------------------------------
                                                         GROSS                                     GROSS
                                                        CARRYING           ACCUMULATED           CARRYING            ACCUMULATED
                                                         AMOUNT           AMORTIZATION            AMOUNT             AMORTIZATION
                                                      -----------         ------------          -----------          ------------
<S>                                                   <C>                  <C>                  <C>                  <C>
Costs of settling patent litigation                   $10,533,248          $ 7,139,252          $10,533,248          $ 6,386,876
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          $ 9,388,363          $12,782,359          $ 8,635,987
                                                      ===========          ===========          ===========          ===========
</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, 2004. The remaining restructuring balance of $1.0 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 sheets
and the remainder is included in other long-term liabilities.

<Table>
<S>                                                               <C>
Accrued restructuring balance at December 31, 2004                $  1,116,848
Payments made                                                          (78,311)
                                                                  ------------
Accrued restructuring balance at June 30, 2005                    $  1,038,537
                                                                  ------------
</Table>

(10) Shareholder's Equity

The Board of Directors has authorized a program for the repurchase by the
Company of up to 5% of its outstanding common stock. Third Wave has repurchased
218,000 shares of common stock as of June 30, 2005 for $877,159.


(11) Reclassifications

Certain reclassifications have been made to the 2004 financial statements to
conform to the 2005 presentation.



                                       8
<PAGE>
                         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, 2005 and for the three and six months ended June 30,
2005 and 2004 should be read in conjunction with our Form 10-K for the fiscal
year ended December 31, 2004 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) chemistry, a novel, proprietary molecular
chemistry is easier to use, more accurate and cost-effective, and enables higher
testing throughput. These and other advantages conferred by our chemistry are
enabling us to provide clinicians and researchers with superior molecular
solutions.

More than 110 clinical laboratory customers are using Third Wave's molecular
diagnostic reagents. 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 test for hepatitis C virus, cystic fibrosis and other inherited
disorders, including the Factor V Leiden and a host of other mutations
associated with cardiovascular and other diseases. The Company has developed and
plans to continue to develop a menu of molecular diagnostic products for
clinical applications that include genetic testing, pharmacogenetics,
oncology/chromosomal analysis, and infectious disease/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. As a result, annual financial results are more indicative
of the Company's performance than quarterly results and results of operations in
any quarterly period may not be indicative of results likely to be realized in
the subsequent quarterly periods.

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 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 have 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



                                       9
<PAGE>

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 quarters ended June 30, 2005 and June 30,
2004, we recorded an impairment charge on certain equipment of $0.2 million and
$0.8 million, respectively.

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.

DERIVATIVE INSTRUMENTS

We sell products in a number of countries throughout the world. During 2005 and
2004, 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, 2005. 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 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, 2005, our
inventory reserves were at $0.7 million, or 25% of our $2.8 million total gross
inventories.

RESULTS OF OPERATIONS

Three and Six Months Ended June 30, 2005 and 2004

REVENUES. Revenues for the three months ended June 30, 2005 of $5.8 million
represented a decrease of $6.8 million, compared to revenues of $12.6 million
for the corresponding period of 2004. Revenues for the six months ended June 30,
2005 of $12.9 million represented a decrease of $15 million, compared to
revenues of $27.9 million for the corresponding period of 2004.

Product revenues decreased to $5.6 million for the quarter ended June 30, 2005,
from $12.5 million in the quarter ended June 30, 2004. Product revenues
decreased to $12.5 million for the six months ended June 30, 2005, from $27.7
million in the six months ended June 30, 2004. The decrease in product sales
during the three and six months ending June 30, 2005 was primarily due to a
decrease in
                                       10
<PAGE>


sales of genomic research product to a major Japanese research institute
partially offset by an increase in clinical molecular diagnostic sales compared
to the corresponding periods of 2004. As we continue to develop and expand our
line of molecular diagnostic products, we expect our molecular diagnostic
revenues to increase.

Significant Customer. We generated $3.5 million, or 27% of our revenues, from
sales to a major Japanese research institute for use by several end-users during
the six months ended June 30, 2005, compared to $19.1 million, or 69% of our
revenues during the six months ended June 30, 2004. We believe this customer
will continue to purchase Company products. However, the timing and amount of
such purchases will be influenced by the Japanese government funding process and
other factors beyond the Company's control, as a result of which the timing and
amount of such purchases 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, 2005, cost of goods sold
decreased to $1.8 million, compared to $3.7 million for the corresponding period
of 2004. For the six months ended June 30, 2005, cost of goods sold decreased to
$3.8 million, compared to $7.9 million for the corresponding period of 2004. The
decrease in the six month period was primarily due to the decrease 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, 2005 were
$2.0 million, compared to $3.0 million for the three months ended June 30, 2004.
Research and development expenses for the six months ended June 30, 2005 were
$4.5 million, compared to $5.7 million for the six months ended June 30, 2004.
The decrease in research and development expenses was primarily due to a
decrease 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, 2005 were $3.2 million, an increase of $0.5 million, compared to $2.7
million for the corresponding period of 2004. Selling and marketing expenses for
the six months ended June 30, 2005 were $6.5 million, an increase of $1.2
million, compared to $5.3 million for the corresponding period of 2004. The
increase in selling and marketing expenses was due to an increase in personnel
related expenses compared to the same period in 2004. We anticipate selling and
marketing expenses to continue to be at or above 2004 levels for the remainder
of 2005 and beyond.

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 $4.3 million in
the three months ended June 30, 2005, from $3.2 million for the corresponding
period in 2004. General and administrative expenses increased to $8.0 million in
the six months ended June 30, 2005, from $5.6 million for the corresponding
period in 2004. The increase in general and administrative expenses was
primarily due to an increase in legal expenses as a result of the patent
infringement lawsuit against Stratagene. The Company anticipates a continued
high level legal expenses until the lawsuit is resolved. As the Company moves
towards consideration of FDA cleared or approved products, there will be
increased expenses attributed to these activities.

IMPAIRMENT. In the three and six months ended June 30, 2005 an impairment charge
of $0.2 million was recorded for the loss on equipment that was sold, compared
to $0.8 million for the three and six months ended June 30, 2004 for equipment
written down to fair value.

INTEREST INCOME. Interest income for the three months ended June 30, 2005 was
$0.4 million, compared to $0.1 million for the corresponding period of 2004.
Interest income for the six months ended June 30, 2005 was $0.7 million compared
to $0.3 million in the six months ended June 30, 2004. The increase in interest
income was due to higher interest rates compared to 2004.

INTEREST EXPENSE. Interest expense for the three months ended June 30, 2005 and
2004 was approximately $0.1 million. Interest expense for the six months ended
June 30, 2005 was $0.2 million compared to $0.1 million in the corresponding
period of 2004.



                                       11
<PAGE>

OTHER INCOME (EXPENSE): Other expense for the three months ended June 30, 2005
was $0.1 million, compared to other income of $0.6 million for the three months
ended June 30, 2004. Other expense for the six months ended June 30, 2005 was
$0.3 million, compared to other expense of $0.1 million for the six months ended
June 30, 2004.

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, product sales, a convertible note and an initial public
offering. As of June 30, 2005, we had cash and cash equivalents and short-term
investments of $61.5 million.

Net cash used in operations for the six months ended June 30, 2005 was $5.4
million, compared to net cash provided by operations of $10.3 million in the
corresponding period in 2004. The decrease in cash provided by operations was
primarily due to an increase in operating losses, as a result of decreased
revenue and increased legal expenses due to the patent infringement lawsuit
against Stratagene.

Net cash used in investing activities for the six months ended June 30, 2005 was
$0.8 million, compared $0.1 million in the corresponding period in 2004.
Investing activities included capital expenditures of $0.2 million in the six
months ended June 30, 2005 and 2004. Investing activities included proceeds from
the sale of equipment of $0.2 million in the six months ended June 30, 2005,
compared to $0.1 million in the corresponding period in 2004. Investing
activities in the six months ended June 30, 2005 also included a net cash usage
of $0.8 million to purchase short-term investments.

Net cash provided by financing activities was $0.2 million in the six months
ended June 30, 2005, compared to $1.0 million in the six months ended June 30,
2004. Cash provided by financing activities in the six months ending June 30,
2005 consisted of proceeds from the sale of common stock under the Company's
employee stock purchase plan and stock option plans of $0.3 million compared to
$0.8 million in the corresponding period of 2004. In the six months ended June
30, 2005, there was $0.8 million of proceeds from long-term debt compared to
$0.2 million in the six months ended June 30, 2004. Additionally, in the six
months ended June 30, 2005, $0.9 million was used to repurchase 218,000 shares
of company stock, $56,000 was used to repay debt, and $42,000 for capital lease
obligations. The Company has a $9,500,000 note payable with a bank due on August
14, 2005, bearing annual interest at 3.36%. The Company intends to renew this
term note upon expiration. The Company also entered into three additional notes
payable in the original amounts of $200,000, $270,000, and $800,000. The notes
have a final maturity date of July 1, 2007, October 1, 2009, and July 1, 2008,
bear annual interest at 4.25%, 4.93%, and 5.2%, respectively, and require
monthly principal and interest payments. The borrowings under the notes payable
are secured by short-term investments consisting of certificates of deposit, of
$10,570,000. The Company has an available and unused $1,300,000 letter of credit
with the same bank that expires on September 1, 2005.

The Company believes that its current cash reserves together with its ability to
establish borrowing arrangements will be sufficient to support the short-term
and long-term liquidity requirements for current operations (including annual
capital expenditures). However, 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:

        -       our progress with our research and development programs;

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

        -       our ability to establish and maintain successful collaborative
                relationships;

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

        -       the timing of purchases of additional capital expenditures.

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.




                                       12
<PAGE>

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 of this Form 10-Q and in the "Overview" and "Risk
Factors" sections of our annual report on Form 10-K for the fiscal year ended
December 31, 2004 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 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.

From time to time, we may be involved in litigation relating to claims arising
out of our operations in the usual course of business.

        On September 15, 2004, Third Wave filed suit against Stratagene
        Corporation in the United States District Court for the Western District
        of Wisconsin. The complaint alleges patent infringement by Stratagene
        Corporation of at least several claims in each of the two Third Wave
        asserted patents concerning the Company's proprietary Invader
        technology. Discovery is currently underway and trial is scheduled for
        August 22, 2005.

        On May 6, 2005, Stratagene Corporation filed suit against Third Wave in
        the United States District Court for the District of Delaware. The
        complaint alleges patent infringement by Third Wave of claims of two
        Stratagene patents. The complaint, which does not specify any allegedly
        infringing products, has not been served on Third Wave as of the date of
        this filing.


ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS.

    (a) None

    (b) 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



                                       13

<PAGE>

        "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, 2005, 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.

(c)  Unregistered Sales of Equity Securities.

                     ISSUER PURCHASES OF EQUITY SECURITIES
<Table>
<Caption>
 -----------------------------------------------------------------------------------------------------------------------------------
                                                                        (C) TOTAL NUMBER OF SHARES
                                    (A) TOTAL NUMBER    (B) AVERAGE        PURCHASED AS PART OF
                                        OF SHARES      PRICE PAID PER   PUBLICLY ANNOUNCED PLANS OR    (D) MAXIMUM NUMBER OF SHARES
 PERIOD                                 PURCHASED          SHARE               PROGRAMS (1)              THAT MAY YET BE PURCHASED
 -----------------------------------------------------------------------------------------------------------------------------------
 <S>                                 <C>                <C>              <C>                            <C>
        April 1 - April 30, 2005                 0            $0.00                             0                         2,024,184

 -----------------------------------------------------------------------------------------------------------------------------------
           May 1 -  May 31, 2005           218,000            $4.02                       218,000                         1,806,184

 -----------------------------------------------------------------------------------------------------------------------------------
          June 1 - June 30, 2005                 0            $0.00                             0                         1,806,184

 -----------------------------------------------------------------------------------------------------------------------------------
                          Total:           218,000            $4.02                       218,000
 -----------------------------------------------------------------------------------------------------------------------------------
</Table>
(1)  Shares were repurchased under a program announced on July 27, 2004 under
     which the Company may repurchase up to 5% of its outstanding common stock.
     The program expires on December 31, 2005 but may be terminated by the Board
     of Directors at any time. No shares were purchased other than through
     publicly announced programs during the periods shown.

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 14, 2005, Lionel
Sterling was elected to serve a three-year term expiring 2008. The voting on
this matter was as follows:

<Table>
<Caption>
Director                         Votes FOR               Votes WITHHELD
<S>                              <C>                     <C>
Lionel Sterling                  39,119,048                  315,137
</Table>

In addition to Mr. Sterling, the term of office of each of the following
directors continued after the meeting: Gordon F. Brunner, Sam Eletr, John Neis,
Lance Fors, John J. Puisis and David A. Thompson.

As reported in the Form 8-K filed by the Company on June 6, 2005, following the
mailing date of the proxy statement for the 2005 Annual Meeting of
Shareholders, the Company appointed Grant Thornton, LLP as the Company's
independent public accounting firm for the 2005 fiscal year. Due to the
appointment of Grant Thornton, LLP, the proposal to ratify the appointment of
Ernst & Young LLP as the Company's independent public accounting firm for the
2005 fiscal year was tabled and not voted on.

ITEM 5. OTHER INFORMATION - None.

ITEM 6. EXHIBITS

    (a) Exhibits.

    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



                                       14
<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, 2005             /s/ John Puisis
                                     ----------------------------
                                     John Puisis, CEO

    Date: August 9, 2005             /s/ James Herrmann
                                     ----------------------------
                                     James Herrmann, Principal Financial Officer



                                       15