<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 March 31, 2006 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)

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

<TABLE>
<S>                                                               <C>
      502 S. ROSA ROAD, MADISON, WI                                 53719
(Address of principal executive offices)                          (Zip Code)
</TABLE>

                                 (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 a large accelerated filer, an
accelerated filer, or a non-accelerated filer. See definition of "accelerated
filer and large accelerated filer" in Rule 12b-2 of Exchange Act. (Check one):

Large Accelerated Filer [ ]   Accelerated Filer [X]   Non-Accelerated Filer [ ]

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 May 5, 2006, was 41,481,882.

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

<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.
                          QUARTERLY REPORT ON FORM 10-Q
                      FOR THE QUARTER ENDED MARCH 31, 2006

                                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 March 31, 2006 (Unaudited) and
         December 31, 2005...........................................       3
      Consolidated Statements of Operations (Unaudited) for the Three
         Months Ended March 31, 2006 and 2005........................       5
      Consolidated Statements of Cash Flows (Unaudited) for the Three
         Months Ended March 31, 2006 and 2005.......... .............       6
      Notes to Consolidated Financial Statements.....................       7
   Item 2. Management's Discussion and Analysis of Financial
      Condition and Results of Operations............................      10
   Item 3. Quantitative and Qualitative Disclosures About Market
      Risk...........................................................      14
   Item 4. Controls and Procedures...................................      15
PART II OTHER INFORMATION............................................      15
   Item 1. Legal Proceedings.........................................      15
   Item 2. Unregistered Sales of Equity Securities and Use of
      Proceeds.......................................................      16
   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>


                                        2

<PAGE>
                         PART I - FINANCIAL INFORMATION
                          ITEM 1. FINANCIAL STATEMENTS
                          THIRD WAVE TECHNOLOGIES, INC.

                           Consolidated Balance Sheets

<TABLE>
<CAPTION>
                                                              March 31,     December 31,
                                                                 2006           2005
                                                            -------------   -------------
                                                              Unaudited
<S>                                                         <C>             <C>
ASSETS
Current assets:
   Cash and cash equivalents                                $  24,566,350   $  27,681,704
   Short-term investments                                      11,035,000      11,035,000
   Accounts  receivable, net of allowance for doubtful
      accounts of $200,000 at March 31, 2006 and December
      31, 2005, respectively                                    3,469,560       3,764,519
   Inventories                                                  3,349,118       2,248,183
   Prepaid expenses and other                                     927,275         235,794
                                                            -------------   -------------
Total current assets                                           43,347,303      44,965,200
Equipment and leasehold improvements:
   Machinery and equipment                                     15,699,826      15,563,119
   Leasehold improvements                                       2,346,946       2,346,938
                                                            -------------   -------------
                                                               18,046,772      17,910,057
   Less accumulated depreciation and amortization              13,543,893      13,192,617
                                                            -------------   -------------
                                                                4,502,879       4,717,440
                                                            -------------   -------------
Restricted cash                                                        --         805,184
Intangible assets, net of accumulated amortization              2,265,432       2,641,620
Indefinite-lived intangible assets                              1,007,411       1,007,411
Goodwill                                                          489,873         489,873
Capitalized license fees                                        3,552,183       2,797,046
Other assets                                                      952,716         980,954
                                                            -------------   -------------
Total assets                                                $  56,117,797   $  58,404,728
                                                            =============   =============
LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities:
   Accounts payable                                         $   7,364,132   $   6,850,207
   Accrued payroll and related liabilities                      2,838,280       2,158,870
   Other accrued liabilities                                    2,196,831       2,344,835
   Deferred revenue                                               125,313         121,497
   Capital lease obligations due within one year                  109,886         114,693
   Long-term debt due within one year                             383,351         378,551
                                                            -------------   -------------
Total current liabilities                                      13,017,793      11,968,653
Long-term debt                                                    542,780         639,564
Deferred revenue - long-term                                      118,119         145,382
Capital lease obligations - long-term                             185,087         191,924
Other liabilities                                               5,356,409       5,384,904
</TABLE>


                                        3

<PAGE>

<TABLE>
<S>                                                         <C>             <C>
Shareholders' equity:
   Participating  preferred stock, Series A, $.001 par
      value, 10,000,000 shares authorized, no shares
      issued and outstanding                                           --              --
   Common stock, $.001 par value, 100,000,000 shares
      authorized, 41,622,827 shares issued, 41,404,827
      shares outstanding at March 31, 2006 and 41,461,377
      shares issued, 41,243,377 shares
      outstanding at December 31, 2005                             41,623          41,461
   Additional paid-in capital                                 200,188,852     199,097,187
   Unearned stock compensation                                         --        (114,892)
   Treasury stock - 218,000 shares acquired at an average
      price of $4.02 per share                                   (877,159)       (877,159)
   Foreign currency translation adjustment                         47,478          47,442
   Accumulated deficit                                       (162,503,185)   (158,119,738)
                                                            -------------   -------------
Total shareholders' equity                                     36,897,609      40,074,301
                                                            -------------   -------------
Total liabilities and shareholders' equity                  $  56,117,797   $  58,404,728
                                                            =============   =============
</TABLE>

          See accompanying notes to consolidated financial statements.


                                        4

<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.

                      Consolidated Statements of Operations
                                   (Unaudited)

<TABLE>
<CAPTION>
                                                        Three Months Ended
                                                            March 31,
                                                    -------------------------
                                                        2006          2005
                                                    -----------   -----------
<S>                                                 <C>           <C>
Revenues:
   Clinical product sales                           $ 4,709,787   $ 3,101,709
   Research product sales                             2,995,688     3,812,567
   License and royalty revenue                           27,263        93,083
   Grant revenue                                        141,882       118,884
                                                    -----------   -----------
Total revenues                                        7,874,620     7,126,243
                                                    -----------   -----------
Operating expenses:
   Cost of goods sold
      Product cost of goods sold                      1,469,650     1,538,676
      Intangible and long-term asset amortization       693,391       461,395
                                                    -----------   -----------
                                                      2,163,041     2,000,071
   Research and development                           2,302,013     2,465,380
   Selling and marketing                              3,028,635     3,364,493
   General and administrative                         4,060,595     3,013,746
   Litigation                                         1,001,934       765,518
                                                    -----------   -----------
Total operating expenses                             12,556,218    11,609,208
                                                    -----------   -----------
Loss from operations                                 (4,681,598)   (4,482,965)
Other income (expense):
   Interest income                                      373,182       347,000
   Interest expense                                     (55,846)      (89,387)
   Other                                                (19,185)     (195,187)
                                                    -----------   -----------
Total other income (expense)                            298,151        62,426
                                                    -----------   -----------
Net loss                                            $(4,383,447)  $(4,420,539)
                                                    ===========   ===========
Net loss per share - basic and diluted              $     (0.11)  $     (0.11)
Weighted average shares outstanding
   Basic                                             41,310,561    41,123,521
   Diluted                                           41,310,561    41,123,521
</TABLE>

          See accompanying notes to consolidated financial statements.


                                        5
<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.

                      Consolidated Statements of Cash Flows
                                   (Unaudited)

<TABLE>
<CAPTION>
                                                      Three Months Ended March 31,
                                                      ----------------------------
                                                            2006          2005
                                                        -----------   -----------
<S>                                                   <C>             <C>
OPERATING ACTIVITIES:
Net loss                                                $(4,383,447)  $(4,420,539)
Adjustments to reconcile net loss to net cash used
   in operating activities:
   Depreciation and amortization                            407,082       459,113
   Amortization of intangible assets                        376,188       376,188
   Amortization of licensed technology                      317,203        85,207
   Noncash stock compensation                               966,546      (414,464)
   Loss on disposal of equipment                              9,691         8,696
   Changes in operating assets and liabilities:
      Accounts receivable                                   302,888     1,282,310
      Inventories                                        (1,100,935)     (152,683)
      Prepaid expenses and other assets                    (621,138)     (378,181)
      Accounts payable                                      157,505       960,041
      Accrued expenses and other liabilities                 70,205      (183,429)
      Deferred revenue                                      (23,447)      157,540
                                                        -----------   -----------
Net cash used in operating activities                    (3,521,659)   (2,220,201)

INVESTING ACTIVITIES:
Purchases of equipment and leasehold improvements          (182,733)      (10,170)

Purchases of licensed technology                           (333,212)           --

Change in restriced cash balance                            805,184            --
                                                        -----------   -----------
Net cash provided by (used in) investing activities         289,239       (10,170)

FINANCING ACTIVITIES:
Payments on long-term debt                                  (91,984)      (28,118)
Payments on capital lease obligations                       (31,123)      (17,555)
Proceeds from issuance of common stock, net                 240,173       116,803
                                                        -----------   -----------
Net cash provided by financing activities                   117,066        71,130
                                                        -----------   -----------

Net decrease in cash and cash equivalents                (3,115,354)   (2,159,241)
                                                        -----------   -----------

Cash and cash equivalents at beginning of period         27,681,704    55,619,981
                                                        -----------   -----------

Cash and cash equivalents at end of period              $24,566,350   $53,460,740
                                                        ===========   ===========
</TABLE>

Noncash investing and financing activities:

During the three months ended March 31, 2006 and 2005, the Company entered into
capital lease obligations of $19,479 and $96,496, respectively.

During the three months ended March 31, 2006 the Company entered into a license
agreement under which the Company will pay 1,000,000 Euros over two years. The
estimated present value of the license is $1,122,338.

          See accompanying notes to consolidated financial statements.


                                        6

<PAGE>
                          THIRD WAVE TECHNOLOGIES, INC.

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                 March 31, 2006
                                   (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, 2006.

The balance sheet at December 31, 2005 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, 2005 filed with the
Securities and Exchange Commission.

(2)  Net Loss Per Share

In accordance with accounting principles generally accepted in the United
States, basic net loss per share has been computed using the weighted-average
number of shares of common stock outstanding during the respective periods.
Diluted net loss per share takes into account the weighted average shares from
options that could potentially dilute basic net income per share in the future.
Shares associated with stock options are excluded for the three months ended
March 31, 2006 and 2005 because they are anti-dilutive.

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

<TABLE>
<CAPTION>
                                                   THREE MONTHS ENDED MARCH 31,
                                                   ----------------------------
                                                        2006          2005
                                                    -----------   -----------
<S>                                                <C>            <C>
Numerator:
   Net loss                                         $(4,383,447)  $(4,420,539)
                                                    ============  ============
Denominator
   Weighted average shares outstanding - basic       41,310,561    41,123,521
   Dilutive securities - stock options                      N/A           N/A
                                                    -----------   -----------
   Weighted average shares outstanding - diluted     41,310,561    41,123,521
Basic net loss per share                            $     (0.11)  $     (0.11)
Dilutive net loss per share                         $     (0.11)  $     (0.11)
</TABLE>

(3)  Stock-Based Compensation

The Company has Incentive Stock Option Plans for its employees and Nonqualified
Stock Option Plans (collectively, the Plans) for employees and non-employees
under which an aggregate of 13,213,183 stock options may be granted. Options
under the Plans have a maximum life of ten years. Options vest at various
intervals, as determined by the Board of Directors at the date of grant.  At
March 31, 2006, approximately 2.2 million shares were available for future grant
under the plans.

The Company also has an Employee Stock Purchase Plan (Purchase Plan) under which
an aggregate of 1,256,800 common shares may be issued. Employees are eligible to
participate in the Purchase Plan if they work at least 20 hours per week and
more than five months in any calendar year. Eligible employees may make
contributions through payroll deductions of up to 10% of their compensation. The
price of common stock purchased under the Purchase Plan is 85% of the lower of
the fair market value of the common stock at the beginning or end of the
offering period. There were no shares sold to employees in the three months
ended March 31, 2006, and 2005. At March 31, 2006, approximately 431,000 shares
were available for issuance under the plan.

The following table summarizes the activity under the Plan for the three months
ended March 31, 2006:

<Table>
<Caption>

                                            NUMBER OF     WEIGHTED EXERCISE
                                             SHARES        EXERCISE PRICE
                                            ---------     -----------------
<S>                                         <C>           <C>
Outstanding at December 31,2005             9,101,298           $ 4.34
  Granted                                     417,000             2.94
  Exercised                                  (161,450)            1.49
  Forfeited                                  (700,546)            5.09
                                            ---------           ------
Outstanding at March 31, 2006               8,656,302           $ 4.27
Options Exercisable at March 31, 2006       5,392,448           $ 4.73
</Table>

The weighted-average fair value of stock options granted in the three months
ended March 31, 2006 and 2005 was $1.89 and $4.93, respectively, using the
Black-Scholes option-pricing model. The calculations were made assuming a
dividend yield of 0%, a weighted-average expected option life of five years and
a weighted-average risk-free interest rate of 4.7%, and 4.5% in 2006 and 2005,
respectively. The volatility factor used in the Black-Scholes model for 2006 and
2005 was 77% and 83%, respectively.

Prior to January 1, 2006, we used the intrinsic value method prescribed in
Accounting Principles Board Opinion No. 25, "Accounting for Stock Issued to
Employees", and related interpretations, in accounting for stock options granted
under our Plans. Generally, no compensation cost was required to be recognized
for options granted to employees because the options had an exercise price equal
to the market value per share of the underlying common stock on the date of
grant. Prior to 2006, the Purchase Plan was considered noncompensatory under APB
Opinion No. 25 and, therefore, no expense was recorded for the 15% discount.

Options granted to non-employee consultants were accounted for in accordance
with SFAS No. 123 and Emerging Issues Task Force (EITF) Issue No. 96-18,
"Accounting for Equity Instruments That Are Issued to Other Than Employees for
Acquiring, or in Conjunction with Selling, Goods or Services," and therefore
were measured based upon their fair value as calculated using the Black-Scholes
option pricing model. The fair value of options granted to non-employees was
periodically remeasured as the underlying options vested.

On January 1, 2006, The Company adopted SFAS No. 123 (revised 2004),
"Share-Based Payment", which is a revision of SFAS No. 123. SFAS No. 123(R)
permits public companies to adopt its requirements using one of two methods: (1)
a "modified prospective" method in which compensation cost is recognized
beginning with the effective date (a) based on the requirements of SFAS No.
123(R) for all-share based payments granted after the effective date and (b)
based on the requirements of SFAS No. 123 for all awards granted to employees
prior to the effective date of SFAS No. 123(R) that remain unvested on the
effective date; or (2) a "modified retrospective" method which includes the
requirements of the modified prospective method described above, but also
permits entities to restate based on the amounts previously recognized under
SFAS No. 123 for purposes of pro forma disclosures either (a) all prior periods
presented or (b) prior interim periods of the year of adoption. The Company has
adopted the modified prospective approach.


                                        7

<PAGE>
As prescribed in the modified prospective approach, prior periods have not been
restated to reflect the effects of implementing FAS 123(R).  For the three month
period ended March 31, 2005, the pro forma stock option expense, net loss and
net loss per share are as follows:

<TABLE>
<S>                                                         <C>
Net loss, as reported                                       $(4,420,539)
   Add: Stock-based compensation, as reported                  (414,464)
   Add: Stock-based compensation, using fair value method    (1,064,014)
                                                            -----------
Pro forma net loss                                          $(5,899,017)
Net loss per share, basic and diluted, as reported          $     (0.11)
Pro forma net loss per share, basic and diluted             $     (0.14)
</TABLE>

(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>
                                             MARCH 31,   DECEMBER 31,
                                               2006          2005
                                            ----------   ------------
<S>                                         <C>          <C>
Raw materials                               $1,992,979    $1,486,166
Finished goods and work in process           2,206,139     1,437,017
Reserve for excess and obsolete inventory     (850,000)     (675,000)
                                            ----------    ----------
Total inventories                           $3,349,118    $2,248,183
                                            ==========    ==========
</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
                                    MARCH 31,
                              --------------------
                                2006        2005
                              --------   ---------
<S>                           <C>        <C>
Cost of goods sold            $ 40,913   $  (5,749)
Research and development       155,790    (259,850)
Selling and marketing          198,946      29,708
General and administrative     570,897    (178,573)
                              --------   ---------
   Total stock compensation   $966,546   $(414,464)
                              --------   ---------
</TABLE>

(6)  Comprehensive Loss

The components of comprehensive loss are as follows:

<TABLE>
<CAPTION>
                                                  THREE MONTHS ENDED
                                                      MARCH 31,
                                              -------------------------
                                                  2006          2005
                                              -----------   -----------
<S>                                           <C>           <C>
Net loss                                      $(4,383,447)  $(4,420,539)
Other comprehensive income (loss):
   Foreign currency translation adjustments            36          (854)
                                              -----------   -----------
Comprehensive loss                            $(4,383,411)  $(4,421,393)
                                              ===========   ===========
</TABLE>


                                        8

<PAGE>

(7)  Amortizable Intangible Assets

Amortizable intangible assets consist of the following:

<TABLE>
<CAPTION>
                                                     MARCH 31, 2006             DECEMBER 31, 2005
                                               --------------------------   --------------------------
                                                  GROSS                        GROSS
                                                 CARRYING     ACCUMULATED     CARRYING     ACCUMULATED
                                                  AMOUNT     AMORTIZATION      AMOUNT     AMORTIZATION
                                               -----------   ------------   -----------   ------------
<S>                                            <C>           <C>            <C>           <C>
Costs of settling patent litigation            $10,533,248    $ 8,267,816   $10,533,248    $ 7,891,628
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    $10,516,927   $12,782,359    $10,140,739
                                               ===========    ===========   ===========    ===========
</TABLE>

(8)  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, 2005. The remaining restructuring balance of $0.9 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, 2005   $957,563
Payments made                                         (41,485)
                                                     --------
Accrued restructuring balance at March 31, 2006      $916,078
                                                     --------
</TABLE>

(9)  Shareholders' Equity

The Board of Directors had 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 December 31, 2005 for $877,159. The program
expired on December 31, 2005.

(10) Reclassifications

Certain reclassifications have been made to the 2005 financial statements to
conform to the 2006 presentation.


                                        9
<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 March 31, 2006 and for the three months ended March 31, 2006
and 2005 should be read in conjunction with our Form 10-K for the fiscal year
ended December 31, 2005 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.

OVERVIEW

Third Wave Technologies, Inc. develops and markets molecular diagnostic reagents
for a variety of DNA and RNA analysis applications to meet the needs of our
customers. The Company offers a number of products based on its Invader (R)
chemistry for clinical testing. Third Wave offers in vitro diagnostic kits and
analyte specific, general purpose, and research use only reagents for nucleic
acid analysis. We believe our proprietary Invader(R) chemistry, a novel,
molecular chemistry, is easier to use, 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 145 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 has received clearance from the U.S. Food and Drug Administration for
its Invader (R) UGT1A1 Molecular Assay. The Invader (R) UGT1A1 Molecular Assay
is used to identify patients who may be at increased risk of adverse reaction to
the chemotherapy Camptosar(R) (irinotecan) by detecting and identifying specific
mutations in the UGT1A1 gene that have been associated with that risk.
Camptosar, marketed in the United States by Pfizer, Inc., is used to treat
colorectal cancer and has been relabeled to include dosing recommendations based
on a patient's genetic profile. The Company also markets a growing number of
products, including analyte specific reagents (ASRs). These ASRs allow certified
clinical reference laboratories to create assays that test for infectious
disease (e.g., hepatitis C virus), inherited disorders (e.g., Factor V Leiden),
and a host of other markers associated with genetic predispositions and other
diseases. The Company has developed or plans to develop a menu of molecular
diagnostic products for clinical applications that include genetic testing,
pharmacogenetics, and 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 submissions for FDA clearances or approvals and intellectual
property litigation.

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.


                                       10

<PAGE>

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 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.

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.

STOCK-BASED COMPENSATION EXPENSE

Prior to 2006, we accounted for share-based payments to employees using APB
Opinion No. 25's intrinsic value method and, as such, generally recognized no
compensation cost for employee stock options when granted. On January 1, 2006 we
adopted SFAS No. 123(R) as a result of which we recognize expense for all
share-based payments to employees, including grants of employee stock options,
based on their fair values. We have adopted the modified prospective transition
method as permitted by SFAS No. 123(R).


                                       11

<PAGE>

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 March 31, 2006, our
inventory reserves were $850,000, or 20% of our $4.2 million total gross
inventories.

RESULTS OF OPERATIONS

Three Months Ended March 31, 2006 and 2005

REVENUES. Revenues for the three months ended March 31, 2006 of $7.9 million
represented an increase of $0.8 million, compared to revenues of $7.1 million
the corresponding period of 2005. Following is a discussion of changes in
revenues:

Total clinical molecular diagnostic product revenue increased to $4.7 million in
the quarter ended March 31, 2006 from $3.1 million in the quarter ended
March 31, 2005. U.S. clinical molecular diagnostic revenue increased to $4.4
million in the three months ended March 31, 2006 from $2.9 million for the
corresponding period in 2005.

Research product revenues decreased to $3.0 million in the three months ended
March 31, 2006 from $3.8 million in the three months ended March 31, 2005. The
decrease in research product sales during 2006 resulted from a decrease in
genomic research product sales to a Japanese research institute for use by
several end users compared to prior year. The decrease in research revenue from
the Japan research institute was partially offset by an increase in revenue from
our Agbio business.

Significant Customer. We generated $2.0 million, or 25% of our revenues, from
sales to a major Japanese research institute for use by several end-users during
the three months ended March 31, 2006, compared to $3.1 million, or 44% of our
revenues during the three months ended March 31, 2005.

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 March 31, 2006, cost of goods sold
increased to $2.2 million, compared to $2.0 million for the corresponding period
of 2005. The increase in the three month period was primarily due to the
increase in sales volume.

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 March 31, 2006 were
$2.3 million, compared to $2.5 million for the three months ended March 31,
2005. The decrease in research and development expenses was primarily due to a
decrease in development expense and material costs for assay development, offset
by an increase in stock based compensation expense of $0.4 million. We will
continue to invest in research and development, and expenditures in this area
may increase as we expand our product development efforts. In addition, as the
Company moves towards consideration of FDA cleared or approved products, there
will be increased expenses attributed to these activities.

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
March 31, 2006 were $3.0 million, a decrease of $0.4 million, compared to $3.4
million for the corresponding period of 2005. The decrease in selling and
marketing expenses was due to a decrease in personnel related and equipment
expense, offset by an increase in stock based compensation expense of $0.2
million compared to the same period in 2005.


                                       12

<PAGE>

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 $4.1 million in
the three months ended March 31, 2006, from $3.0 million for the corresponding
period in 2005. The increase in general and administrative expense was due to an
increase in personnel related expenses, legal fees, and a $0.7 million increase
in stock based compensation expense.

LITIGATION EXPENSE. Litigation expense consists of legal fees and other costs
associated with patent infringement and other lawsuits. Litigation expense
increased to $1.0 million in the three months ended March 31, 2006 from $0.8
million in the corresponding period in 2005. The increase was a result of the
additional lawsuits with Innogenetics, Chiron Corporation, Bayer Corporation,
Digene Corporation and Stratagene. With the exception of Stratagene, these
lawsuits were resolved in the quarter ending March 31, 2006, and we anticipate
litigation expense to be below the 2005 levels for the remainder of the year.

INTEREST INCOME. Interest income for the three months ended March 31, 2006 was
$0.4 million, compared to $0.3 million for the corresponding period of 2005. The
increase in interest income was due to higher interest rates compared to 2005.

INTEREST EXPENSE. Interest expense for the three months ended March 31, 2006 and
2005 was approximately $0.1 million.

OTHER INCOME (EXPENSE): Other expense for the three months ended March 31, 2006
was approximately $19,000 compared to $0.2 million for the same period in 2005.
The decrease in other expense was primarily due to the adjustments related to
foreign currency transactions in the three months ended March 31, 2005.

OTHER ITEMS- SUBSEQUENT EVENT: On March 31, 2006, Third Wave Technologies Japan,
K.K., a Japanese corporation ("Third Wave Japan") and wholly-owned subsidiary of
Third Wave Technologies, Inc. (the "Company"), entered into a Series A Preferred
Stock and Warrant Purchase Agreement (the "Purchase Agreement") with Mitsubishi
Corporation ("Mitsubishi") and CSK Institute for Sustainability, LTD., a wholly
owned subsidiary of CSK Holdings ("CSK" and, together with Mitsubishi, the
"Investors"). Under the Purchase Agreement, Mitsubishi agreed to invest (Y)480
million (approximately $4.2 million) and CSK agreed to invest (Y)100 million
(approximately $800,000) in Third Wave Japan in exchange for convertible, Series
A preferred stock of Third Wave Japan and warrants to purchase an additional
(Y)100 million (approximately $800,000) worth of Third Wave Japan common stock.
Upon completion of the transactions contemplated under the Purchase Agreement,
the Investors will own approximately 17% of Third Wave Japan prior to the
exercise of the warrant or 20% after exercise of the warrant. The transaction
was completed on April 21, 2006.

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 March 31, 2006, we had cash and cash equivalents and short-term
investments of $35.6 million.

Net cash used in operations for the three months ended March 31, 2006 was $3.5
million, compared to $2.2 million in the corresponding period in 2005. The
change was primarily due to an increase in inventories.

Net cash provided by investing activities for the three months ended March 31,
2006 was $0.3 million, compared to net cash used of $10,000 in the corresponding
period in 2005. Investing activities included capital expenditures of $0.2
million in the three months ended March 31, 2006 versus $10,000 for the same
period in 2005. Investing activities in the three months ended March 31, 2006
included the payment on license fee arrangements of $0.3 million and a change in
the restricted cash balance of $0.8 million.

Net cash provided by financing activities was $0.1 million in the three months
ended March 31, 2006 and 2005. Cash provided by financing activities in the
three months ending March 31, 2006 consisted of proceeds from the sale of common
stock under the Company's employee stock purchase plan and stock option plans of
$0.2 million compared to $0.1 million in the corresponding period of 2005. In
the three months ended March 31, 2006, $0.1 million was used to repay debt,
compared to $28,000 in the same period in 2005. Additionally, in the three
months ended March 31, 2006 and 2005, $31,000 and $18,000 was used for capital
lease obligations, respectively.


                                       13

<PAGE>

The Company has three notes payable to a bank in the original amounts of
$200,000, $270,000, and $800,000. These 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 $1,000,000. The Company has an available and unused $1,300,000 letter
of credit with the same bank that expires on September 1, 2006.

We believe that current cash reserves together with our ability to establish
borrowing arrangements will be sufficient to support 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;

     -    the needs we may have to pursue FDA clearances or approvals of our
          products;

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

     -    our ability to establish and maintain successful collaborative
          relationships;

     -    the costs we incur in securing intellectual property rights, whether
          through patents, licenses or otherwise;

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

     -    the need to respond to competitive pressures;

     -    the possible acquisition of complementary products, businesses or
          technologies; and

     -    the timing of 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 discussed
under the heading "Overview" in the Management's Discussion and Analysis of
Financial Condition and Results of Operations section of this Form 10-Q and in
the "Risk Factors" and Management's Discussion and Analysis of Financial
Condition and Results of Operations sections of our annual report on Form 10-K
for the fiscal year ended December 31, 2005 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. Our exposure to market risk was discussed in the
Quantitative and Qualitative Disclosures About Market Risk section of our annual
report on Form 10-K for the fiscal


                                       14

<PAGE>

year ended December 31, 2005 filed with the Securities and Exchange Commission.
There have been no material changes to such exposures during the first quarter
of 2006.

ITEM 4. CONTROLS AND PROCEDURES

As required by Rule 13a-15(b) under the Securities Exchange Act of 1934, the
Company's management, including our 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, our 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. There have been no
significant changes during the period covered by this report in the Company's
internal control over financial reporting that have materially affected, or are
reasonably likely to materially affect, internal controls over financial
reporting.

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.

In September 2004, we filed a suit against Stratagene Corporation in the United
States District Court for the Western District of Wisconsin. The complaint
alleged patent infringement of two of our patents concerning our proprietary
Invader technology by Stratagene's sale of its QPCR and QRTPCR Full Velocity
products. The case was tried before a jury in August 2005, and the jury found
that Stratagene willfully infringed our patents and that our patents were valid.
The jury awarded us $5.29 million in damages. The Court subsequently entered a
permanent injunction barring Stratagene from making, selling or offering to sell
its Full Velocity QPCR and QRT-PCR products and any other products that practice
our patented Invader methods. In December 2005, the Court tripled the damages
award to $15.9 million and ruled that Stratagene must pay attorney fees of $4.2
million. In January 2006, the Court awarded additional interest on the damages
award in the amount of $485,716, increasing the total damages amount to $16.4
million. Also in January 2006, Stratagene posted a $21 million civil bond to
stay payment of the judgment while it conducts its appeal. Stratagene has
appealed the verdict, the award of enhanced damages, and the award of attorneys'
fees and costs to the Court of Appeals for the Federal Circuit in Washington,
D.C.

In May 2005, Stratagene Corporation filed suit against us in the United States
District Court for the District of Delaware. The complaint alleges patent
infringement of claims of two Stratagene patents relating to our Invader Plus
chemistry. The complaint was served on us in September 2005. A trial date of
November 5, 2007 was set by the Court.

In September 2005, Innogenetics filed suit against us in the United States
District Court for the Western District of Wisconsin. The complaint alleged that
our HCVg ASRs infringe a patent owned by Innogenetics relating to the detection
of the hepatitis C virus. In February 2006, we reached an agreement with
Innogenetics that resolved the litigation. In connection with the agreement,
Third Wave acquired a non-exclusive license to Innogenetics' patent for the
United States. The agreement includes certain opt-out rights for Third Wave, as
well as an option to extend both the term and global reach of the license.

In October 2005, we filed a declaratory judgment suit in the United States
District Court for the Western District of Wisconsin against Digene Corporation
seeking a ruling that our HPV ASRs do not infringe any valid claims of Digene's
human papillomavirus related patents. In January 2006, we reached an agreement
with Digene to dismiss the suit without prejudice. We also agreed that neither
party would file a suit against the other relating to the Digene human
papillomavirus patents for one year.

Also in October 2005, we filed a declaratory judgment suit in the United States
District Court for the Western District of Wisconsin against Chiron Corporation
and Bayer Corporation seeking a ruling that our HCVg ASRs do not infringe any
valid claims of Chiron's hepatitis C related patents. In February 2006, we
reached an agreement with Chiron and Bayer to dismiss the suit without
prejudice. No license were granted or taken under the agreement and no payment
of any monies was made to any of the companies.

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


                                       15

<PAGE>

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 1A. RISK FACTORS

There have been no material changes in our risk factors from those disclosed in
our Form 10-K for the fiscal year ended December 31, 2005 filed with the
Securities and Exchange Commission.

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 "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 March 31, 2006, 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 $35.2 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

ITEM 3. DEFAULTS UPON SENIOR SECURITIES - None.

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

ITEM 5. OTHER INFORMATION.

On February 14, 2006, the Company's board of directors established the Company's
Long Term Incentive Plan No. 3. Under the plan, awards were made to select
employees, including the Company's executive officers, covering the 2006-2008
period to provide a continued emphasis on specified financial performance goals
which the board considers to be important contributors to long-term stockholder
value. These cash awards will be payable only if the Company achieves specified
goals over the performance period for the following three measurements: the
Company's total shareholder return ranking as compared to its peer group, the
Company's stock price growth and the growth in the Company's clinical molecular
diagnostics revenue. A copy of the plan was filed as Exhibit 10.29 to the
Company's annual report on Form 10-K for the fiscal year ended December 31, 2005
filed with the Securities and Exchange Commission and is hereby incorporated by
reference herein. The foregoing description of the plan does not purport to be
complete and is qualified in its entirety by reference to the full text of the
plan.

ITEM 6. EXHIBITS

The exhibits required to be filed as a part of this Report are listed in the
Exhibit Index


                                       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: May 4, 2006                      /s/ Kevin Conroy
                                        ----------------------------------------
                                        Kevin Conroy, Chief Executive Officer


Date: May 4, 2006                      /s/ Maneesh Arora
                                        ----------------------------------------
                                        Maneesh Arora,  Chief Financial Officer


                                       17

<PAGE>

                                  EXHIBIT INDEX

<TABLE>
<CAPTION>
EXHIBIT
  NO.                      DESCRIPTION                            INCORPORATED BY REFERENCE TO
-------                    -----------                            ----------------------------
<S>      <C>                                             <C>
  3.1    Amended and Restated Bylaws of the Registrant   Exhibit 3.1 to Registrant's Current Report on
                                                         Form 8-K filed April 17, 2006

 10.1    Severance Agreement between James J. Herrmann   Exhibit 10.26 to Registrant's Annual Report
         and Third Wave Technologies, Inc. dated         on Form 10-K for the fiscal year ended
         January 31, 2006                                December 31, 2005

 10.2    Third Wave Technologies, Inc. LTIP 3 dated      Exhibit 10.29 to Registrant's Annual Report
         February 14, 2006                               on Form 10-K for the fiscal year ended
                                                         December 31, 2005

 10.3    Series A Preferred Stock and Warrant Purchase
         Agreement between Registrant, Mitsubishi
         Corporation and CSK Institute for
         Sustainability, LTD., dated April 21, 2006

 10.4    Investor Rights Agreement between Registrant,
         Third Wave Technologies Japan, KK, Mitsubishi
         Corporation and CSK Institute for
         Sustainability, LTD., dated April 21, 2006

 31.1    CEO's Certification Pursuant to Section 302 of
         the Sarbanes Oxley Act of 2002

 31.2    CFO's Certification pursuant to Section 302 of
         the Sarbanes Oxley Act of 2002.

 32      CEO and CFO Certification pursuant to 18 U.S.C.
         Section 1350, of Chapter 63 of Title 18 of the
         United States Code

</TABLE>


                                       18