<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 September 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 [ ]

Indicate by check mark whether the registrant is a shell company (as defined in
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 November 4, 2005, was 41,236,377.

================================================================================



<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.
                          QUARTERLY REPORT ON FORM 10-Q
                    FOR THE QUARTER ENDED SEPTEMBER 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 September 30, 2005 and December 31, 2004.......................................   3
     Consolidated Statements of Operations for the three and nine months ended September 30, 2005 and 2004............   4
     Consolidated Statements of Cash Flows for the nine months ended September 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.................................................  13
   Item 4. Controls and Procedures....................................................................................  14
PART II OTHER INFORMATION.............................................................................................  14
   Item 1. Legal Proceedings..........................................................................................  14
   Item 2. Unregistered Sales of Equity Securities and Use of Proceeds................................................  14
   Item 3. Defaults Upon Senior Securities............................................................................  16
   Item 4. Submission Of Matters To A Vote Of Security Holders........................................................  16
   Item 5. Other Information..........................................................................................  16
   Item 6. Exhibits...................................................................................................  16
SIGNATURES............................................................................................................  17
EXHIBITS
</TABLE>
<PAGE>
                         PART I - FINANCIAL INFORMATION
                          ITEM 1. FINANCIAL STATEMENTS
                          THIRD WAVE TECHNOLOGIES, INC.
                         Consolidated Balance Sheets


<TABLE>
<CAPTION>
                                                                    September 30, 2005       December 31, 2004
                                                                       (Unaudited)
<S>                                                                 <C>                      <C>
ASSETS
Current assets:
  Cash and cash equivalents                                           $  42,431,168            $  55,619,981
  Short-term investments                                                 11,835,000               11,070,000
  Receivables, net of allowance for doubtful accounts
    of $185,000 and $300,000 at September 30, 2005
    and December 31, 2004, respectively                                   3,642,717                5,784,679
  Inventories                                                             2,234,084                1,236,392
  Prepaid expenses and other                                                650,148                  260,316
                                                                      -------------            -------------
Total current assets                                                     60,793,117               73,971,368

Equipment and leasehold improvements:
  Machinery and equipment                                                15,453,981               15,832,489
  Leasehold improvements                                                  2,347,093                2,277,604
                                                                      -------------            -------------
                                                                         17,801,074               18,110,093
  Less accumulated depreciation                                          12,792,956               12,139,423
                                                                      -------------            -------------
                                                                          5,008,118                5,970,670
                                                                      -------------            -------------

Assets held for sale                                                              -                  269,000
Intangible assets, net of accumulated amortization                        3,017,808                4,146,372
Indefinite lived intangible assets                                        1,007,411                1,007,411
Goodwill                                                                    489,873                  489,873
Other long term assets                                                    1,857,730                2,212,935
                                                                      -------------            -------------

Total assets                                                          $  72,174,057            $  88,067,629
                                                                      =============            =============

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities:
  Accounts payable                                                    $   6,169,092            $   6,519,005
  Accrued payroll and related liabilities                                 1,936,319                2,873,506
  Other accrued liabilities                                               3,286,377                1,867,361
  Deferred revenue                                                          213,269                  129,530
  Capital lease obligation                                                  104,095                   66,867
  Long-term debt due within one year                                      9,873,800                9,614,127
                                                                      -------------            -------------
Total current liabilities                                                21,582,952               21,070,396

Long-term debt                                                              749,356                  335,069
Deferred revenue - long term                                                172,645                  254,434
Capital lease obligations - long term                                       209,283                  151,885
Other liabilities                                                         4,581,460                3,520,948

Shareholders' equity:
  Participating preferred stock, Series A, $.001 par value,
   10,000,000 shares authorized, 0 shares issued and outstanding                  -                        -
  Common stock, $.001 par value, 100,000,000 shares authorized,
   41,370,234 shares issued, 41,152,234 shares outstanding at
  September 30, 2005 and 41,102,764 shares issued and outstanding
   at December 31, 2004                                                      41,370                   41,103
  Additional paid-in capital                                            199,073,727              198,990,162
  Unearned stock compensation                                              (312,277)                (554,293)
  Treasury stock - 218,000 shares acquired at an average price
   of $4.02 per share                                                      (877,159)                       -
  Foreign currency translation adjustment                                    41,136                   31,949
  Accumulated deficit                                                  (153,088,436)            (135,774,024)
                                                                      -------------            -------------
Total shareholders' equity                                               44,878,361               62,734,897
                                                                      -------------            -------------

Total liabilities and shareholders' equity                            $  72,174,057            $  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:                  Nine Months Ended:
                                                          September 30,                       September 30,
                                                    2005             2004              2005               2004
                                                ------------      ------------      ------------      ------------
<S>                                             <C>               <C>               <C>               <C>
Revenues:
  Clinical product sales                          $  4,031,766      $  3,828,240      $ 11,407,180      $ 10,284,198
  Research product sales                             1,039,569         6,496,157         6,152,540        27,783,714
  License and royalty revenue                           89,763            71,492           272,609           167,121
  Grant revenue                                         61,293            83,138           287,819           151,870
                                                  ------------      ------------      ------------      ------------

Total revenues                                       5,222,391        10,479,027        18,120,148        38,386,903
                                                  ------------      ------------      ------------      ------------

Operating expenses:
  Cost of goods sold
  Product cost of goods sold                         1,108,385         1,813,702         3,960,294         8,565,560
  Intangible and long-term asset amortization          468,035           521,505         1,427,625         1,634,160
                                                  ------------      ------------      ------------      ------------
  Total cost of goods sold                           1,576,420         2,335,207         5,387,919        10,199,720

  Research and development                           2,063,762         3,026,445         6,569,300         8,726,631
  Selling and marketing                              3,662,014         2,370,231        10,208,077         7,691,222
  General and administrative                         5,600,641         2,863,852        13,647,600         8,433,456
  Impairment charge                                          -                 -           202,707           758,716
                                                  ------------      ------------      ------------      ------------

Total operating expense                             12,902,837        10,595,735        36,015,603        35,809,745
                                                  ------------      ------------      ------------      ------------

Income (loss) from operations                       (7,680,446)         (116,708)      (17,895,455)        2,577,158

Other income (expense):
  Interest income                                      459,704           210,997         1,200,042           480,945
  Interest expense                                    (128,516)          (74,030)         (313,278)         (189,779)
  Other                                                (30,685)            4,015          (305,721)         (101,357)
                                                  ------------      ------------      ------------      ------------
Total other income (expense)                           300,503           140,982           581,043           189,809

Net income (loss)                                 $ (7,379,943)     $     24,274      $(17,314,412)     $  2,766,967

Net income (loss) per share - basic               $      (0.18)     $       0.00      $      (0.42)     $       0.07
Net income (loss) per share - diluted             $      (0.18)     $       0.00      $      (0.42)     $       0.07
Weighted average shares outstanding
  Basic                                             41,073,652        40,521,411        41,094,740        40,309,084
  Diluted                                           41,073,652        42,509,345        41,094,740        42,070,075

</TABLE>


          See accompanying notes to consolidated financial statements.



                                       4
<PAGE>


                          THIRD WAVE TECHNOLOGIES, INC.

                      Consolidated Statements of Cash Flows
                                   (Unaudited)


<TABLE>
<CAPTION>
                                                                    Nine Months Ended September 30,
                                                                        2005              2004
<S>                                                                 <C>               <C>
OPERATING ACTIVITIES:
Net income (loss)                                                   $(17,314,412)     $  2,766,967
Adjustments to reconcile net income (loss) to net cash provided
by (used in) operating activities:
  Depreciation and amortization                                        1,596,997         2,103,010
  Amortization of intangible assets                                    1,128,564         1,128,564
  Noncash stock compensation                                            (354,827)        1,329,404
  Impairment charge and loss on disposal of equipment                    208,731           870,058
  Changes in operating assets and liabilities:
    Receivables                                                        2,084,109        (1,658,382)
    Inventories                                                         (997,692)          124,122
    Prepaid expenses and other assets                                   (266,647)          121,605
    Accounts payable                                                    (349,913)          629,801
    Accrued expenses and other liabilities                             1,542,341           161,368
    Deferred revenue                                                       1,950           421,237
                                                                    ------------      ------------
Net cash provided by (used in) operating activities                  (12,720,799)        7,997,754

INVESTING ACTIVITIES:
Purchases of equipment and leasehold improvements                       (307,185)         (532,601)
Proceeds on sale of equipment                                            197,287            65,020
Purchases of short-term investments                                  (11,835,000)      (11,070,000)
Sales and maturities of short-term investments                        11,070,000        10,800,000
                                                                    ------------      ------------
Net cash used in investing activities                                   (874,898)         (737,581)

FINANCING ACTIVITIES:
Proceeds of long-term debt                                               800,000           470,000
Payments on long-term debt                                              (126,040)          (10,399)
Payment on capital lease obligations                                     (70,591)                -
Proceeds from common stock, net                                          680,674         1,332,168
Repurchase of stock                                                     (877,159)                -
                                                                    ------------      ------------
Net cash provided by financing activities                                406,884         1,791,769

Net increase (decrease) in cash and cash equivalents                 (13,188,813)        9,051,942

Cash and cash equivalents at beginning of period                      55,619,981        47,015,746

Cash and cash equivalents at end of period                          $ 42,431,168      $ 56,067,688
</TABLE>




During the nine months ended September 30, 2005, the Company entered into
capital lease obligations of $165,217.



          See accompanying notes to consolidated financial statements.


                                       5
<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                               September 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 nine months ended September 30, 2005 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 SEPTEMBER 30,    NINE MONTHS ENDED SEPTEMBER 30,
                                                           2005              2004             2005              2004
                                                      ------------      -------------     -------------     ------------
<S>                                                   <C>               <C>               <C>               <C>
Numerator:
    Net income (loss)                                 $ (7,379,943)     $     24,274      $(17,314,412)     $  2,766,967
Denominator
    Weighted average shares outstanding - basic         41,073,652        40,521,411        41,094,740        40,309,084
    Dilutive securities - stock options                        N/A         1,987,934               N/A         1,760,991
    Weighted average shares outstanding - diluted       41,073,652        42,509,345        41,094,740        42,070,075
Basic net income (loss) per share                     $      (0.18)     $      (0.00)     $      (0.42)     $       0.07
Dilutive net income (loss) per share                  $      (0.18)     $      (0.00)     $      (0.42)     $       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 SEPTEMBER 30,     NINE MONTHS ENDED SEPTEMBER 30,
                                                                2005               2004            2005                2004
                                                          --------------      -----------     --------------      -------------
<S>                                                       <C>                 <C>             <C>                 <C>
Net income (loss), as reported                            $   (7,379,943)     $   24,274      $  (17,314,412)     $   2,766,967
  Add: Stock-based compensation, as reported                     422,357         785,226            (354,827)         1,329,404
  Less: Stock-based compensation, using fair value
   method                                                     (1,217,295)       (814,730)         (3,557,025)       (3,013,856)
  Less: Stock-based compensation, related to the
   employee stock purchase plan determined under SFAS
   No. 123                                                           -0-             -0-             (95,847)          (151,017)
                                                          --------------      ----------      --------------      -------------
Pro forma net income (loss)                               $   (8,174,881)     $   (5,230)     $  (21,322,111)           931,498
                                                          ==============      ==========      ==============      =============
Net income (loss) per share, basic, as reported           $        (0.18)     $    (0.00)     $        (0.42)     $        0.07
Net income (loss) per share, diluted, as reported         $        (0.18)     $    (0.00)     $        (0.42)     $        0.07
Pro forma net income (loss) per share, basic              $        (0.20)     $    (0.00)     $        (0.52)     $        0.02
Pro forma net income (loss) per share, diluted            $        (0.20)     $    (0.00)     $        (0.52)     $        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>
                                                            SEPTEMBER 30,      DECEMBER 31,
                                                                2005               2004
                                                           --------------    ----------
<S>                                                        <C>                 <C>
Raw materials                                              $   1,630,456       $  1,318,771
Finished goods and work in process                             1,363,628            567,621
Reserve for excess and obsolete inventory                       (760,000)          (650,000)
                                                           -------------       ------------
Total inventories                                          $   2,234,084       $  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                NINE MONTHS ENDED
                                                  SEPTEMBER 30,                     SEPTEMBER 30,
                                             2005             2004             2005             2004
                                         ------------     -----------      ------------    -------------
<S>                                      <C>              <C>              <C>             <C>
Cost of goods sold                       $     40,143     $    47,731      $     27,163    $      57,692
Research and development                        1,969         419,025          (499,113)         769,970
Selling and marketing                          33,150             188            45,557           68,674
General and administrative                    347,095         318,282            71,566          433,068
                                         ------------     -----------      ------------    -------------
  Total stock compensation               $    422,357     $   785,226      $   (354,827)   $   1,329,404
                                         ------------     -----------      ------------    -------------
</TABLE>


(6) Comprehensive Income (Loss)

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


<TABLE>
<CAPTION>
                                                           THREE MONTHS ENDED                 NINE MONTHS ENDED
                                                              SEPTEMBER 30,                     SEPTEMBER 30,
                                                         2005             2004             2005              2004
                                                     --------------    -----------    --------------   -------------
<S>                                                  <C>               <C>            <C>              <C>
Net income (loss)                                    $  (7,379,943)    $   24,274      $(17,314,412)    $   2,766,967
Other comprehensive income (loss):
  Foreign currency translation adjustments                   4,625         (1,945)             9,187           (1,774)
                                                     -------------     ----------      -------------    -------------
Comprehensive income (loss)                          $  (7,375,318)    $   22,329      $ (17,305,225)   $   2,765,193
                                                     =============     ==========      =============    =============
</TABLE>




                                       7
<PAGE>

(7) Derivative Instruments

We sell products in a number of countries throughout the world. In the quarters
ended September 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 September 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>
                                                               SEPTEMBER 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        $   7,515,440      $   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        $   9,764,551      $   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                                                      (118,768)
                                                                ------------
Accrued restructuring balance at September 30, 2005             $   998,080
                                                                ------------
</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 September 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 September 30, 2005 and for the three and nine months ended
September 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 discussion below
under the caption "Forward-Looking Statements".

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 120 clinical laboratory customers are using Third Wave's products.
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, human papillomavirus, 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 recently received FDA clearance of its UGT1A1 pharmacogenetic test,
which is designed to detect mutations associated with adverse reaction to the
chemotherapy Camptosar. The Company has developed and plans to continue to
develop a menu of molecular diagnostic products for clinical applications that
include genetics/pharmacogenetics, oncology/chromosomal analysis, and infectious
disease/women's health. The Company also has a number of other Invader(R)
products 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.



                                       9
<PAGE>

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.

REVENUE RECOGNITION

Revenue from product sales is recognized upon delivery which is generally when
the title passes to the customer, provided that the Company has completed all
performance obligations and the customer has accepted the products. Customers
have no contractual rights of return or refunds associated with product sales.
Consideration received in multiple element arrangements is allocated to the
separate units based upon their relative fair values.

Grant and development revenues consist primarily of research grants from
agencies of the federal government and revenue from companies with which the
Company has established strategic alliances, the revenue from which is
recognized as research is performed. Payments received which are related to
future performance are deferred and recorded as revenue when earned. Grant
payments designated to purchase specific assets to be used in the performance of
a contract are recognized as revenue over the shorter of the useful life of the
asset acquired or the contract.

License and royalty revenue includes amounts earned from third parties for
licenses of the Company's intellectual property and are recognized when earned
under the terms of the related agreements. License revenues are generally
recognized upon receipt unless the Company has continuing performance
obligations, in which case the license revenue is recognized ratably over the
period of expected performance.

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 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



                                       10
<PAGE>

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 nine months ended September 30, 2005 and September
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. In the quarter ended September 30,
2005, the annual impairment test was performed and 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 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 September 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 September 30, 2005, our
inventory reserves were at $0.8 million, or 25% of our $3.0 million total gross
inventories.

RESULTS OF OPERATIONS

Three and Nine Months Ended September 30, 2005 and 2004

REVENUES. Revenues for the three months ended September 30, 2005 of $5.2 million
represented a decrease of $5.3 million, compared to revenues of $10.5 million
for the corresponding period of 2004. Revenues for the nine months ended
September 30, 2005 of $18.1 million represented a decrease of $20.3 million,
compared to revenues of $38.4 million for the corresponding period of 2004.

Product revenues decreased to $5.1 million for the quarter ended September 30,
2005, from $10.3 million in the quarter ended September 30, 2004. Product
revenues decreased to $17.6 million for the nine months ended September 30,
2005, from $38.1 million in the nine months ended September 30, 2004. The
decrease in product sales during the three and nine months ending September 30,
2005 was primarily due to a decrease in 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 $3.6 million, or 20% of our revenues, from
sales to a major Japanese research institute for use by several end-users during
the nine months ended September 30, 2005, compared to $25.0 million, or 65% of
our revenues during the nine months ended September 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 September 30, 2005, cost of goods
sold decreased to $1.6 million, compared to $2.3 million for the corresponding
period of 2004. For the nine months ended



                                       11
<PAGE>

September 30, 2005, cost of goods sold decreased to $5.4 million, compared to
$10.2 million for the corresponding period of 2004. The decrease in the nine
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 September 30, 2005
were $2.1 million, compared to $3.0 million for the three months ended September
30, 2004. Research and development expenses for the nine months ended September
30, 2005 were $6.6 million, compared to $8.7 million for the nine months ended
September 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
September 30, 2005 were $3.7 million, an increase of $1.3 million, compared to
$2.4 million for the corresponding period of 2004. Selling and marketing
expenses for the nine months ended September 30, 2005 were $10.2 million, an
increase of $2.5 million, compared to $7.7 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 $5.6 million in
the three months ended September 30, 2005, from $2.9 million for the
corresponding period in 2004. General and administrative expenses increased to
$13.6 million in the nine months ended September 30, 2005, from $8.4 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 of legal expenses as a result of the additional lawsuits
with Innogenetics, Chiron Corporation, Bayer Corporation, Digene Corporation and
Stratagene discussed in further detail below in Part II - Item 1 "Legal
Proceedings." In addition, as the Company moves towards consideration of FDA
cleared or approved products, there will be increased expenses attributed to
these activities.

IMPAIRMENT. In the nine months ended September 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 nine months ended September 30, 2004 for equipment written
down to fair value.

INTEREST INCOME. Interest income for the three months ended September 30, 2005
was $0.5 million, compared to $0.2 million for the corresponding period of 2004.
Interest income for the nine months ended September 30, 2005 was $1.2 million
compared to $0.5 million in the nine months ended September 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 September 30, 2005
and 2004 was approximately $0.1 million. Interest expense for the nine months
ended September 30, 2005 was $0.3 million compared to $0.2 million in the
corresponding period of 2004.

OTHER INCOME (EXPENSE): Other expense for the three months ended September 30,
2005 was approximately $31,000 compared to other income of approximately $4,000
for the same period in 2004. Other expense for the nine months ended September
30, 2005 was $0.3 million, compared to other expense of $0.1 million for the
nine months ended September 30, 2004.

OTHER ITEMS: On September 14, 2004, Third Wave filed suit against Stratagene
Corporation in the United States District Court for the Western District of
Wisconsin. The complaint alleged patent infringement by Stratagene's sale of its
QPCR; QRTPCR Full Velocity products of two Third Wave patents concerning the
Company's proprietary Invader technology. The case was tried before a jury in
August 2005 and the jury found that Stratagene willfully infringed Third Wave's
patents, and that Third Wave's patents were valid. The jury awarded Third Wave
$5.29 million in damages. Post-trial motions are currently pending before the
Court, including Stratagene's motion for a new trial and to resolve the damages
award and Third Wave's motion for trebled damages, attorneys fees and costs.
Stratagene may post a bond with the court pending appellate review in lieu of
paying Third Wave any awarded damages or costs. The appellate review is expected
to take between 1-3 years.





                                       12
<PAGE>

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 September 30, 2005, we had cash and cash equivalents and
short-term investments of $54.3 million.

Net cash used in operations for the nine months ended September 30, 2005 was
$12.7 million, compared to net cash provided by operations of $8.0 million in
the corresponding period in 2004. The decrease in cash provided by operations
was primarily due to an increase in operating losses.

Net cash used in investing activities for the nine months ended September 30,
2005 was $0.9 million, compared $0.7 million in the corresponding period in
2004. Investing activities included capital expenditures of $0.3 million in the
nine months ended September 30, 2005 versus $0.5 million for the same period in
2004. Investing activities included proceeds from the sale of equipment of $0.2
million in the nine months ended September 30, 2005, compared to $0.1 million in
the corresponding period in 2004. Investing activities in the nine months ended
September 30, 2005 also included net cash usage of $0.8 million to purchase
short-term investments, compared to $0.3 million in 2004.

Net cash provided by financing activities was $0.4 million in the nine months
ended September 30, 2005, compared to $1.8 million in the nine months ended
September 30, 2004. Cash provided by financing activities in the nine months
ending September 30, 2005 consisted of proceeds from the sale of common stock
under the Company's employee stock purchase plan and stock option plans of $0.7
million compared to $1.3 million in the corresponding period of 2004. In the
nine months ended September 30, 2005, there was $0.8 million of proceeds from
long-term debt compared to $0.5 million in the nine months ended September 30,
2004. Additionally, in the nine months ended September 30, 2005, $0.9 million
was used to repurchase 218,000 shares of company stock; $126,000 was used to
repay debt; and $71,000 was used for capital lease obligations.

The Company has a $9,500,000 note payable with a bank due on August 14, 2006,
bearing annual interest at 5.17%. Interest on this note is payable monthly and
principal is payable at maturity. The Company has three additional notes payable
in the original amounts of $200,000, $270,000, and $800,000. These additional
notes have respective final maturity dates 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 in the aggregate amount of $10,535,000. The Company has an available and
unused $1,300,000 letter of credit with the same bank that expires on September
1, 2006.

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.

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. We expressly disclaim any obligation or undertaking to release
publicly any updates or revisions to any forward-looking statements contained
herein to reflect any change in our expectations with regard thereto or any
change in events, conditions, or circumstances on which any such statements are
based.

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.



                                       13
<PAGE>

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.

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 14, 2004, Third Wave filed suit against Stratagene Corporation
    in the United States District Court for the Western District of Wisconsin.
    The complaint alleged patent infringement by Stratagene's sale of its QPCR;
    QRTPCR Full Velocity products of two Third Wave patents concerning the
    Company's proprietary Invader technology. The case was tried before a jury
    in August 2005 and the jury found that Stratagene willfully infringed Third
    Wave's patents, and that Third Wave's patents were valid. The jury awarded
    Third Wave $5.29 million in damages. Post-trial motions are currently
    pending before the Court, including Stratagene's motion for a new trial and
    to resolve the damages award and Third Wave's motion for trebled damages,
    attorneys fees and costs.

    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 relating to its Invader Plus
    chemistry of claims of two Stratagene patents. The complaint was served on
    Third Wave in early September. Discovery is expected to begin in the near
    future. No trial date has been set by the Court.

    On September 29, 2005, Innogenetics filed a suit against the Company in the
    United States District Court for the Western District of Wisconsin. The
    complaint alleges that the Company's HCVg ASRs infringe a patent owned by
    Innogenetics relating to the detection of the hepatitis C virus. No trial
    date has been set.

    In October 2005, the Company filed a declaratory judgment suit in the United
    States District Court for the Western District of Wisconsin against Chiron
    Corporation and Bayer Corporation asking the Court for a ruling that the
    Company's HCVg ASRs do not infringe any valid claims of Chiron's hepatitis C
    related patents. No trial date has been set.

    Also in October 2005, the Company filed a declaratory judgment suit in the
    United States District Court for the Western District of Wisconsin against
    Digene Corporation asking the court for a ruling that the Company's HPV ASRs
    do not infringe any valid claims of Digene's human papillomavirus related
    patents. No trial date has been set.

    The Company intends to vigorously pursue its infringement claims against
    third parties and to vigorously defend itself against infringement claims
    brought against it by third parties. There can be no assurance, however,
    that the Company will prevail in these proceedings and should the outcome of
    any of these actions be unfavorable, the Company's business, financial
    condition, results of operations and cash flows could be materially
    adversely affected.

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

    (a) None



                                       14
<PAGE>

    (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 "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 September 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 $16.5 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) None



                                       15
<PAGE>

ITEM 3. DEFAULTS UPON SENIOR SECURITIES - None.

ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS - None.

ITEM 5. OTHER INFORMATION

    On August 14, 2005, we entered into an Amendment to Loan Agreement and Note
    with U.S. Bank N.A. with respect to our $9,500,000 note payable to U.S.
    Bank. Under the terms of the amendment, the note's maturity date was
    extended from August 14, 2005 to August 14, 2006 and the annual interest
    rate was increased to 5.17%. A copy of this Amendment to Loan Agreement is
    filed with this report as Exhibits 10.1 and is incorporated herein by
    reference.

    On October 25, 2005 Sam Eletr resigned from the Board of Directors.


ITEM 6. EXHIBITS

    10.1 Term Loan Agreement dated as of August 14, 2003 between the Company and
         U.S. Bank N.A.

    10.2 $9,500,000 Term Note payable to U.S. Bank N.A dated August 14, 2003

    10.3 Amendment to Loan Agreement and Note dated as of August 14, 2005
         between the Company and U.S. Bank N.A.

    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


                                       16
<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: November 7, 2005                   /s/ John Puisis
                                             -----------------------------------
                                             John Puisis, CEO

    Date: November 7, 2005                   /s/ James Herrmann
                                             -----------------------------------
                                             James Herrmann,
                                             Principal Financial Officer



                                       17