<PAGE>

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

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                    FORM 10-Q

(Mark One)

|X|  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE
     ACT OF 1934 FOR THE QUARTERLY PERIOD ENDED June 30, 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)


                  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 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 August 4, 2006, was 41,700,882.

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


<PAGE>




                          THIRD WAVE TECHNOLOGIES, INC.
                          QUARTERLY REPORT ON FORM 10-Q
                       FOR THE QUARTER ENDED JUNE 30, 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 June 30, 2006 (Unaudited) and December 31, 2005.................................        3
      Consolidated Statements of Operations (Unaudited) for the Three and Six Months Ended June 30, 2006 and 2005.......        4
      Consolidated Statements of Cash Flows (Unaudited) for the Six Months Ended June 30, 2006 and 2005.................        5
      Notes to Consolidated Financial Statements (Unaudited)............................................................        6
    Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations.......................       11
    Item 3. Quantitative and Qualitative Disclosures About Market Risk..................................................       17
    Item 4. Controls and Procedures.....................................................................................       17
PART II OTHER INFORMATION...............................................................................................       17
    Item 1. Legal Proceedings...........................................................................................       17
    Item 2. Unregistered Sales of Equity Securities and Use of Proceeds.................................................       18
    Item 3. Defaults Upon Senior Securities.............................................................................       18
    Item 4. Submission Of Matters To A Vote Of Security Holders.........................................................       18
    Item 5. Other Information...........................................................................................       18
    Item 6. Exhibits....................................................................................................       18
SIGNATURES..............................................................................................................       19
EXHIBITS................................................................................................................       20
</TABLE>




                                       2
<PAGE>
                         PART I - FINANCIAL INFORMATION
                          ITEM 1. FINANCIAL STATEMENTS
                          THIRD WAVE TECHNOLOGIES, INC.
                           Consolidated Balance Sheets


<TABLE>
<CAPTION>
                                                                                         June 30, 2006         December 31, 2005
                                                                                         -------------         -----------------
                                                                                          (Unaudited)
<S>                                                                                      <C>                   <C>
ASSETS
Current assets:
  Cash and cash equivalents                                                              $  25,195,805             $  27,681,704
  Short-term investments                                                                    11,035,000                11,035,000
  Accounts receivables, net of allowance for doubtful accounts of $200,000 at
  June 30, 2006 and December 31, 2005, respectively                                          4,177,432                 3,764,519
  Inventories                                                                                3,288,072                 2,248,183
  Prepaid expenses and other                                                                   829,479                   235,794
                                                                                         -------------             -------------
Total current assets                                                                        44,525,788                44,965,200

  Equipment and leasehold improvements:
  Machinery and equipment                                                                   15,870,871                15,563,119
  Leasehold improvements                                                                     2,363,472                 2,346,938
                                                                                         -------------             -------------
                                                                                            18,234,343                17,910,057
  Less accumulated depreciation and amortization                                            13,929,656                13,192,617
                                                                                         -------------             -------------
                                                                                             4,304,687                 4,717,440
                                                                                         -------------             -------------
Restricted cash                                                                                     --                   805,184
Intangible assets, net of accumulated amortization                                           1,889,244                 2,641,620
Indefinite-lived intangible assets                                                           1,007,411                 1,007,411
Goodwill                                                                                       489,873                   489,873
Capitalized license fees                                                                     3,240,375                 2,797,046
Other assets                                                                                   887,354                   980,954
                                                                                         -------------             -------------
Total assets                                                                             $  56,344,732             $  58,404,728
                                                                                         =============             =============

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities:
  Accounts payable                                                                       $   5,844,860             $   6,850,207
  Accrued payroll and related liabilities                                                    2,944,769                 2,158,870
  Other accrued liabilities                                                                  2,920,109                 2,344,835
  Deferred revenue                                                                             121,725                   121,497
  Capital lease obligations due within one year                                                137,699                   114,693
  Long-term debt due within one year                                                           388,226                   378,551
                                                                                         -------------             -------------
Total current liabilities                                                                   12,357,388                11,968,653
Long-term debt                                                                                 442,889                   639,564
Deferred revenue - long-term                                                                    90,856                   145,382
Capital lease obligations - long-term                                                          159,727                   191,924
Other liabilities                                                                            5,100,405                 5,384,904
Minority interest in subsidiary                                                                663,209

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, 41,699,881
  shares issued, 41,481,881 shares outstanding at June 30, 2006 and 41,461,377
  shares issued, 41,243,377 shares outstanding at December 31, 2005                             41,700                    41,461
  Additional paid-in capital                                                               205,593,626               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                                                        2,135                    47,442
  Accumulated deficit                                                                     (167,230,044)             (158,119,738)
                                                                                         -------------             -------------
Total shareholders' equity                                                                  37,530,258                40,074,301
                                                                                         -------------             -------------
Total liabilities and shareholders' equity                                               $  56,344,732             $  58,404,728
                                                                                         =============             =============
</TABLE>

          See accompanying notes to consolidated financial statements.


                                       3
<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.
                      Consolidated Statements of Operations
                                (Unaudited)
<TABLE>
<CAPTION>

                                                        Three Months Ended June 30,               Six Months Ended June 30,
                                                           2006                2005                 2006                 2005
                                                   ------------------------------------      ------------------------------------
<S>                                                   <C>                  <C>                  <C>                  <C>
Revenues:
   Clinical product sales ....................        $  5,058,561         $  4,273,707         $  9,768,348         $  7,375,414
   Research product sales ....................           1,632,261            1,300,402            4,627,949            5,112,971
   License and royalty revenue ...............              27,263               89,763               54,526              182,846
   Grant revenue .............................              40,994              107,642              182,876              226,526
                                                      ------------         ------------         ------------         ------------
Total revenues ...............................           6,759,079            5,771,514           14,633,699           12,897,757
                                                      ------------         ------------         ------------         ------------

Operating expenses:
   Cost of goods sold
   Product cost of goods sold ................           1,209,886            1,313,230            2,679,536            2,851,909
   Intangible and long-term asset amortization             687,994              498,194            1,381,385              959,590
                                                      ------------         ------------         ------------         ------------
                                                         1,897,880            1,811,424            4,060,921            3,811,499
   Research and development ..................           3,032,584            2,040,159            5,334,597            4,505,538
   Selling and marketing .....................           2,892,154            3,181,569            5,920,789            6,546,063
   General and administrative ................           3,885,711            2,553,916            7,946,306            5,567,659
   Litigation ................................             180,928            1,713,782            1,182,862            2,479,300
   Impairment of equipment ...................                   -              202,707                    -              202,707
                                                      ------------         ------------         ------------         ------------
 Total operating expense .....................          11,889,257           11,503,557           24,445,475           23,112,766
                                                      ------------         ------------         ------------         ------------
Loss from operations .........................          (5,130,178)          (5,732,043)          (9,811,776)         (10,215,009)

Other income (expense):
   Interest income ...........................             373,728              393,338              746,910              740,338
   Interest expense                                        (50,336)             (95,376)            (106,182)            (184,762)
   Other                                                    39,081              (79,849)              19,896             (275,036)
                                                      ------------         ------------         ------------         ------------
Total other income (expense) .................             362,473              218,113              660,624              280,540
                                                      ------------         ------------         ------------         ------------

Net loss before minority interest                     $ (4,767,705)        $ (5,513,930)        $ (9,151,152)        $ (9,934,469)
                                                      ------------         ------------         ------------         ------------

   Minority interest .........................        $     40,846              $   -           $     40,846              $   -
                                                      ------------         ------------         ------------         ------------
Net loss .....................................        $ (4,726,859)        $ (5,513,930)        $ (9,110,306)        $ (9,934,469)
                                                      ============         ============         ============         ============

Net loss per share - basic and diluted .......        $      (0.11)        $      (0.13)        $      (0.22)        $      (0.24)
Weighted average shares outstanding
   Basic and diluted                                    41,460,010           41,087,554           41,384,388           41,105,285

</TABLE>

          See accompanying notes to consolidated financial statements.




                                       4
<PAGE>
                         THIRD WAVE TECHNOLOGIES, INC.

                     Consolidated Statements of Cash Flows
                                  (Unaudited)
<Table>
<Caption>
                                                                                      Six Months Ended June 30,
                                                                                      2006                2005
                                                                                  ------------        -------------
<S>                                                                               <C>                 <C>
OPERATING ACTIVITIES:
Net loss                                                                          $ (9,110,306)       $  (9,934,469)

Adjustments to reconcile net loss to net cash used in operating activities:
  Minority Interest in net loss of subsidiary                                          (40,846)                   -
  Depreciation and amortization                                                        817,834              882,480
  Amortization of intangible assets                                                    752,376              752,376
  Amortization of licensed technology                                                  629,009              207,214
  Noncash stock compensation                                                         1,785,650             (777,184)
  Impairment charge and (gain) loss on disposal of equipment                            27,886              211,403
  Changes in operating assets and liabilities:
    Accounts receivable                                                               (448,148)           1,902,566
    Inventories                                                                     (1,039,889)            (830,541)
    Prepaid expenses and other assets                                                 (460,153)            (152,575)
    Accounts payable                                                                (1,509,668)           2,193,549
    Accrued expenses and other liabilities                                             975,203               35,257
    Deferred revenue                                                                   (54,298)              95,743
                                                                                  ------------        -------------
Net cash used in operating activities                                               (7,675,350)          (5,414,181)

INVESTING ACTIVITIES:
Purchases of equipment and leasehold improvements                                     (374,308)            (150,436)
Proceeds on sale of equipment                                                                -              193,231
Purchases of licensed technology                                                      (516,546)                   -
Purchases of short-term investments                                                          -             (800,000)
Change in restricted cash balance                                                      805,184                    -
                                                                                  ------------        -------------
Net cash used in investing activities                                                  (85,670)            (757,205)

FINANCING ACTIVITIES:
Proceeds from long-term debt                                                                 -              800,000
Payments on long-term debt                                                            (187,000)             (56,422)
Payments on capital lease obligations                                                  (67,850)             (41,530)
Proceeds from issuance of common stock, net                                            435,998              349,717
Proceeds from minority investment in subsidiary                                      5,093,973                    -
Repurchase of common stock for treasury                                                      -             (877,159)
                                                                                  ------------        -------------
Net cash provided by financing activities                                            5,275,121              174,606
                                                                                  ------------        -------------
Net decrease in cash and cash equivalents                                           (2,485,899)          (5,996,780)
                                                                                  ------------        -------------
Cash and cash equivalents at beginning of period                                    27,681,704           55,619,981
                                                                                  ------------        -------------
Cash and cash equivalents at end of period                                        $ 25,195,805        $  49,623,201
                                                                                  ============        =============
</Table>

Noncash investing and financing activities:

During the six months ended June 30, 2006 and 2005, the Company entered into
capital lease obligations of $58,659 and $148,346, respectively.

During the six months ended June 30, 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.

                                       5
<PAGE>




                          THIRD WAVE TECHNOLOGIES, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                  June 30, 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 and six months
ended June 30, 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                SIX MONTHS ENDED
                                                                             JUNE 30                          JUNE 30
                                                                ---------------------------------     ----------------------------
                                                                     2006               2005            2006              2005
                                                                --------------     --------------     ------------   -------------
<S>                                                             <C>                <C>                <C>            <C>
Numerator:
  Net loss                                                      $   (4,726,859)    $  (5,513,930)     $(9,110,306)   $ (9,934,469)
                                                                ==============     ==============     ============   =============
Denominator
  Weighted average shares outstanding -- basic                      41,460,010        41,087,554       41,384,388      41,105,285
  Dilutive securities - stock options                                      N/A               N/A              N/A             N/A
                                                                           ---               ---              ---             ---
  Weighted average shares outstanding -- diluted                    41,460,010        41,087,554       41,384,388      41,105,285
Basic net loss per share                                        $       (0.11)     $       (0.13)     $     (0.22)    $     (0.24)
Dilutive net loss per share                                     $       (0.11)     $       (0.13)     $     (0.22)    $     (0.24)
</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 June
30, 2006, approximately 2.2 million shares were available for future grant under
the plans.

The following table summarizes the activity under the Plans for the six months
ended June 30, 2006:



                                       6
<PAGE>

<TABLE>
<CAPTION>
                                                                                              WEIGHTED
                                                                                               AVERAGE        AGGREGATE
                                                     NUMBER OF        WEIGHTED AVERAGE       CONTRACTUAL      INTRINSIC
                                                      SHARES           EXERCISE PRICE           LIFE            VALUE
                                                    ----------        ----------------       -----------      ---------
<S>                                                 <C>                <C>                   <C>              <C>
Outstanding at December 31,2005                      9,101,298               $   4.34
  Granted                                              754,000                   2.91
  Exercised                                           (171,237)                  1.55
  Forfeited                                         (1,150,126)                  4.78
                                                    ----------        ----------------
Outstanding at June 30, 2006                         8,533,935               $   4.20            6.4          1,461,480
Options Exercisable at June 30, 2006                 5,784,188               $   4.56            5.6          1,150,602

</TABLE>


The weighted-average fair value of stock options granted in the six months ended
June 30, 2006 and 2005 was $1.87 and $3.06, 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 4.95%, and 4.25% in 2006 and 2005,
respectively. The volatility factor used in the Black-Scholes model for 2006 and
2005 was 75% and 82%, respectively. As of June 30, 2006, there was approximately
$5.1 million of total unrecognized compensation cost related to the stock
options granted under the plans. The intrinsic value of the shares exercised in
the six months ended June 30, 2006 and 2005 was $0.2 million and $0.3 million,
respectively.

The Company's stock plan also permits the granting of restricted stock units to
eligible employees and non-employee directors. Restricted stock units are
payable in shares of Company stock upon vesting. The restricted stock units vest
at various intervals as determined by the Board of Directors at the date of
grant. The following table presents a summary of the Company's nonvested
restricted stock units granted to employees as of June 30, 2006.

<TABLE>
<CAPTION>
                                                                                    SIX MONTHS ENDED JUNE 30, 2006

                                                                                    NUMBER OF      WEIGHTED AVERAGE
                                                                                     SHARES           FAIR VALUE


<S>                                                                              <C>                   <C>
           Nonvested shares of restricted stock units at December 31, 2005                  -          $         -
              Granted                                                                 112,530                 2.84
              Vested                                                                        -                    -
              Forfeited                                                                     -                    -
                                                                                  -----------          -----------
           Nonvested shares of restricted stock units at June 30, 2006                112,530          $      2.84
                                                                                  ===========          ===========
</TABLE>

As of June 30, 2006, there was approximately $0.3 million of total unrecognized
compensation cost related to the nonvested restricted stock units granted under
the plan. The expense is expected to be recognized over the vesting period.
Compensation expense related to restricted stock units was approximately $7,000
in the six months ended June 30, 2006. As of June 30, 2006, there were 112,530
restricted stock units outstanding.

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 67,267 and 57,428 shares sold to employees in the
six months ended June 30, 2006, and 2005, respectively. At June 30, 2006,
approximately 364,000 shares were available for issuance under the Purchase
Plan.

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.

Prior to January 1, 2006, 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



                                       7
<PAGE>

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.

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 and
six month periods ended June 30, 2005, the pro forma stock option expense, net
loss and net loss per share are as follows:

<TABLE>
<CAPTION>

                                                                                               Three Months        Six Months
                                                                                             ---------------    ---------------
<S>                                                                                          <C>               <C>
Net loss, as reported                                                                        $   (5,513,930)   $    (9,934,469)
  Add: Stock-based compensation, as reported                                                       (362,720)          (777,184)
  Add: Stock-based compensation, using fair value method                                         (1,275,716)        (2,339,730)
  Add: Stock-based compensation, related to the employee stock purchase plan determined
   under SFAS No. 123                                                                               (95,847)           (95,847)
                                                                                             ---------------    ---------------
Pro forma net loss                                                                           $   (7,248,213)   $   (13,147,230)
                                                                                             ===============    ==============
Net loss per share, basic and diluted, as reported                                           $        (0.13)   $         (0.24)
Pro forma net loss per share, basic and diluted                                              $        (0.18)   $         (0.32)

</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>
                                                                                                JUNE 30,         DECEMBER 31,
                                                                                                  2006              2005
                                                                                             ---------------   ---------------
<S>                                                                                          <C>               <C>
Raw materials                                                                                $    2,126,385      $   1,486,166
Finished goods                                                                                    1,685,617          1,271,101
Work in process                                                                                     406,070            165,916
Reserve for excess and obsolete inventory                                                          (930,000)          (675,000)
                                                                                             ---------------   ---------------
Total inventories                                                                            $    3,288,072    $     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                    SIX MONTHS ENDED
                                                                        JUNE 30,                             JUNE 30,

                                                                 2006             2005               2006               2005
                                                             ------------     ------------       ------------     ------------
<S>                                                          <C>              <C>                <C>              <C>
Cost of goods sold                                           $   21,396        $   (7,231)        $   62,309        $  (12,980)
Research and development                                        165,120          (241,232)           320,910          (501,082)
Selling and marketing                                           182,560           (17,301)           381,506            12,407
General and administrative                                      450,028           (96,956)         1,020,925          (275,529)
                                                             ----------        ----------         ----------        ----------
  Total stock compensation                                   $  819,104        $ (362,720)        $1,785,650        $ (777,184)

</TABLE>

(6) Comprehensive Loss

The components of comprehensive loss are as follows:

<TABLE>
<CAPTION>

                                                              THREE MONTHS ENDED                         SIX MONTHS ENDED
                                                                    JUNE 30,                                 JUNE 30,
                                                               2006              2005               2006               2005
                                                         ------------        ------------        ------------       ------------
<S>                                                      <C>                   <C>               <C>                 <C>
Net loss                                                 $(4,726,859)        $(5,513,930)        $(9,110,306)        $(9,934,469)
Other comprehensive income (loss):
  Foreign currency translation adjustments                   (45,343)              5,416             (45,307)              4,562
                                                         ------------        ------------       ------------         ------------
Comprehensive loss                                       $(4,772,202)        $(5,508,514)        $(9,155,613)        $(9,929,907)
                                                         ============        ============       ============        =============

</TABLE>


                                       8
<PAGE>



(7) Amortizable Intangible Assets

Amortizable intangible assets consist of the following:

<TABLE>
<CAPTION>

                                                                            JUNE 30, 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   $    8,644,004  $  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   $   10,893,115  $  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                                                                     (80,302)
                                                                             ------------
Accrued restructuring balance at June 30, 2006                               $    877,261
                                                                             ============
</TABLE>


(9) Other Long-term Liabilities

Other long-term liabilities consist of the long-term portion of the following
items:

<TABLE>
<CAPTION>

                                                   June 30, 2006       December 31, 2005
                                                   -------------       -----------------
<S>                                                  <C>                 <C>
License payments                                     $1,532,413               $1,430,942
Long-term Incentive Plan                              1,388,332                1,312,841
Restructuring                                           694,690                  775,174
Rent                                                  1,152,854                1,159,094
Other                                                   332,116                  706,853
                                                   -------------       -----------------
                                                     $5,100,405               $5,384,904
                                                   =============       =================
</TABLE>


                                       9
<PAGE>



(10) 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.

(11) New Accounting Pronouncements

In June 2006, the FASB issued FIN No. 48, "Accounting for Uncertainty in Income
Taxes," which clarifies the accounting for uncertainty in income taxes
recognized in an enterprise's financial statements in accordance with SFAS No.
109, "Accounting for Income Taxes." This interpretation prescribes a recognition
threshold and measurement attribute for the financial statement recognition and
measurement of a tax position taken or expected to be taken in a tax return.
This interpretation also provides guidance on derecognition, classification,
interest and penalties, accounting in interim periods, disclosure, and
transition. FIN No. 48 is effective for fiscal years beginning after December
15, 2006. The adoption of Interpretation No. 48 is not expected to have any
significant effect on the Company's consolidated financial position or results
of operations.


(12) Reclassifications

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


                                       10
<PAGE>

                          THIRD WAVE TECHNOLOGIES, INC.

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

This Management's Discussion and Analysis of Financial Condition and Results of
Operations as of June 30, 2006 and for the three and six months ended June 30,
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.

Approximately 150 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. Our
customer base is dominated by a small number of large clinical testing labs. We
regularly experience pricing and other competitive pressures in these accounts.
If for any reason, we are unable to maintain or renew our contracts,
particularly our contracts with key customers, or if, for any reason, we are
unable to maintain current pricing levels and/or volumes with our customers, or
are unable to manufacture the required product, our revenues and business may
suffer materially.

Third Wave has received clearance from the U.S. Food and Drug Administration
(FDA) 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(R), 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. We also market 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 FDA is currently reviewing draft guidance for the
regulation of ASRs.  This guidance would affect the entire in-vitro medical
device sector in which Third Wave competes. If the FDA issues guidance or takes
other actions that limit ASRs throughout the industry or limits Third Wave's
ASRs, it could materially affect our business. 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.

Currently, one of our key strategic initiatives is the commercialization of our
Human Papillomavirus (HPV) offering. To bring this product to market we will
need to receive premarket approval, known as a PMA, from the FDA. Seeking a PMA
for our HPV offering (and for any other product offerings) will be costly and
there can be no assurance that we will receive FDA approval or that other
difficulties will not delay or prevent the successful commercialization of our
HPV offering. If we are unable to successfully commercialize our HPV offering,
our business and prospects may be materially adversely affected. Additionally,
we anticipate significant competition in the HPV market as additional large
competitors have announced plans to enter the market in the near future. This
competition may have a significant impact on the success of our
commercialization of our HPV offering.

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


                                       11
<PAGE>



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. The multiple element
arrangements involve contracts with customers in which the Company is selling
reagent products and leasing equipment to the customer for use during the term
of the contract. Based upon the guidance in paragraph 9 of EITF No. 00-21
"Revenue Arrangements with Multiple Deliverables", both the reagents and
equipment have value to the customer on a standalone basis, there is objective
and reliable evidence of fair value for both the reagents and equipment and
there are no rights of return. The Company has sold both the reagents and
equipment separately, and therefore is able to determine a fair value for each.
The respective fair values are used to allocate the proceeds received to each of
the elements for purposes of recognizing revenue.


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 include 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


                                       12
<PAGE>



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).

INVENTORIES--SLOW MOVING AND OBSOLESCENCE

Significant management judgment is required to determine the reserve for
obsolete or excess inventory. Inventory on hand may exceed future demand either
because of process improvements or technology advancements, the amount on hand
is more than can be used to meet future need, or estimates of shelf lives may
change. We currently consider all inventory that we expect will have no activity
within one year as well as any additional specifically identified inventory to
be subject to a provision for excess inventory. We also provide for the total
value of inventories that we determine to be obsolete based on criteria such as
changing manufacturing processes and technologies. At June 30, 2006, our
inventory reserves were $930,000, or 22% of our $4.2 million total gross
inventories.

NEW ACCOUNTING PRONOUNCEMENTS

On December 16, 2004, the Financial Accounting Standards Board (FASB) issued
SFAS No. 123 (revised 2004), "Share-Based Payment," which is a revision of SFAS
No. 123. SFAS No. 123(R) supersedes APB Opinion No. 25 and amends SFAS No. 95,
"Statement of Cash Flows." Generally, the approach in SFAS No. 123(R) is similar
to the approach described in SFAS No. 123. However, SFAS No. 123(R) requires all
share-based payments to employees, including grants of employee stock options,
to be recognized in the income statement based on their fair values. Pro forma
disclosure is no longer an alternative.

The Company adopted SFAS No. 123(R) on January 1, 2006. 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 adopted the modified
prospective approach.

In June 2006, the FASB issued FIN No. 48, "Accounting for Uncertainty in Income
Taxes," which clarifies the accounting for uncertainty in income taxes
recognized in an enterprise's financial statements in accordance with SFAS No.
109, "Accounting for Income Taxes." This interpretation prescribes a recognition
threshold and measurement attribute for the financial statement recognition and
measurement of a tax position taken or expected to be taken in a tax return.
This interpretation also provides guidance on derecognition, classification,
interest and penalties, accounting in interim periods, disclosure, and
transition. FIN No. 48 is effective for fiscal years beginning after December
15, 2006. The adoption of Interpretation No. 48 is not expected to have any
significant effect on the Company's consolidated financial position or results
of operations.

RESULTS OF OPERATIONS

Three and Six Months Ended June 30, 2006 and 2005

REVENUES. Revenues for the three months ended June 30, 2006 of $6.8 million
represented an increase of $1.0 million, compared to revenues of $5.8 million
for the corresponding period of 2005. Revenues for the six months ended June 30,
2006 of $14.6 million



                                       13
<PAGE>
represented an increase of $1.7 million, compared to revenues of $12.9 million
for the corresponding period of 2005. Following is a discussion of changes in
revenues:

Clinical molecular diagnostic product revenue increased to $5.1 million in the
quarter ended June 30, 2006 from $4.3 million in the quarter ended June 30,
2005. Clinical molecular diagnostic product revenue increased to $9.8 million in
the six months ended June 30, 2006 from $7.4 million in the six months ended
June 30, 2005.

Research product revenues increased to $1.6 million in the three months ended
June 30, 2006 from $1.3 million in the three months ended June 30, 2005.
Research product revenues decreased to $4.6 million in the six months ended June
30, 2006 from $5.1 million in the six months ended June 30, 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. The decrease in research revenue from the Japanese research institute was
partially offset by an increase in revenue from our Agbio business.

Significant Customer. We generated $2.7 million, or 18% of our revenues, from
sales to a major Japanese research institute for use by several end-users during
the six months ended June 30, 2006, compared to $3.5 million, or 27% of our
revenues during the six months ended June 30, 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 June 30, 2006, cost of goods sold
increased to $1.9 million, compared to $1.8 million for the corresponding period
of 2005. For the six months ended June 30, 2006, cost of goods sold increased to
$4.1 million, compared to $3.8 million for the corresponding period of 2005. The
increase in the three and six month periods was primarily due to the increase in
sales volume and amortization of new licenses.

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, including
clinical trials to validate the performance of our products and enhancement of
our products, and acquisition of technologies used or to be used in our
products. Research and development costs are expensed as they are incurred.
Research and development expenses for the three months ended June 30, 2006 were
$3.0 million, compared to $2.0 million for the three months ended June 30, 2005.
Research and development expenses for the six months ended June 30, 2006 were
$5.3 million, compared to $4.5 million for the six months ended June 30, 2005.
The increase in research and development expenses was primarily due to an
increase in development expense, material costs for assay development, and an
increase in stock based compensation expense of $0.4 million and $0.8 million in
the three and six month periods, respectively, compared to the same periods in
2005. 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
June 30, 2006 were $2.9 million, a decrease of $0.3 million, compared to $3.2
million for the corresponding period of 2005. Selling and marketing expenses for
the six months ended June 30, 2006 were $5.9 million, a decrease of $0.6
million, compared to $6.5 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 and $0.4 million in the three and six month periods,
respectively, compared to the same periods in 2005.

GENERAL AND ADMINISTRATIVE EXPENSES. General and administrative expenses consist
primarily of salaries and related expenses for executive, finance and other
administrative personnel, legal and professional fees, office support and
depreciation. General and administrative expenses increased to $3.9 million in
the three months ended June 30, 2006, from $2.6 million for the corresponding
period in 2005. General and administrative expenses increased to $7.9 million in
the six months ended June 30, 2006, from $5.6 million for the corresponding
period in 2005. The increase in general and administrative expense was due to an
increase in legal fees related to our patents and the equity investment in our
Japan subsidiary, a sales tax charge and an increase in stock based compensation
expense of $0.5 million and $1.3 million in the three and six month periods,
respectively compared to the same periods in 2005.

LITIGATION EXPENSE. Litigation expense consists of legal fees and other costs
associated with patent infringement and other lawsuits. Litigation expense
decreased to $0.2 million in the three months ended June 30, 2006 from $1.7
million in the corresponding


                                       14
<PAGE>
period in 2005. Litigation expense decreased to $1.2 million in the six months
ended June 30, 2006 from $2.5 million in the corresponding period in 2005. The
decreases were the result of the decreased litigation activity due to the
resolution of the lawsuits with Innogenetics, Chiron Corporation, Bayer
Corporation, and Digene Corporation. We anticipate litigation expense to be
below the 2005 levels for the remainder of the year.

IMPAIRMENT. In the three and six months ended June 30, 2005 an impairment charge
of $0.2 million was recorded for the loss on equipment that was sold.

INTEREST INCOME. Interest income for the three months ended June 30, 2006 and
2005 was $0.4 million. Interest income for the six months ended June 30, 2006
and 2005 was $0.7 million.

INTEREST EXPENSE. Interest expense for the three months ended June 30, 2006 and
2005 was approximately $0.1 million. Interest expense for the six months ended
June 30, 2006 and 2005 was $0.1 million and $0.2 million, respectively.

OTHER INCOME (EXPENSE). Other income for the three months ended June 30, 2006
was approximately $39,000 compared to expense of $0.1 million for the same
period in 2005. Other income for the six months ended June 30, 2006 was
approximately $20,000 compared to expense of $0.3 million for the same period in
2005. The increase in other income was primarily due to the adjustments related
to foreign currency transactions in the periods.

MINORITY INTEREST. Minority interest for the three and six months ended
June 30, 2006 was $41,000. Minority interest represents Third Wave Japan's
minority investors' share of the equity and earnings of the subsidiary.

LIQUIDITY AND CAPITAL RESOURCES

Since our inception, we have financed our operations primarily through private
placements of equity securities, research grants from federal and state
government agencies, payments from strategic collaborators, equipment loans,
capital leases, product sales, a convertible note and an initial public
offering. As of June 30, 2006, we had cash and cash equivalents and short-term
investments of $36.2 million.

Net cash used in operations for the six months ended June 30, 2006 was $7.7
million, compared to $5.4 million in the corresponding period in 2005. The
change was primarily due to an increase in inventories and decrease in payables.

Net cash used in investing activities for the six months ended June 30, 2006 was
$0.1 million, compared to $0.8 million in the corresponding period in 2005.
Investing activities included capital expenditures of $0.4 million in the six
months ended June 30, 2006 versus $0.2 million for the same period in 2005.
Investing activities in the six months ended June 30, 2006 included the payment
on license fee arrangements of $0.5 million and a change in the restricted cash
balance of $0.8 million. Investing activities in the six months ended June 30,
2005 also included proceeds from the sale of equipment of $0.2 million and the
purchase of short-term investments of $0.8 million.

Net cash provided by financing activities was $5.3 million in the six months
ended June 30, 2006 compared to $0.2 million in 2005. Cash provided by financing
activities in the six months ending June 30, 2006 consisted of proceeds from the
sale of common stock under the Company's employee stock purchase plan and stock
option plans of $0.4 million compared to $0.3 million in the corresponding
period of 2005. In the six months ended June 30, 2006, $0.2 million was used to
repay debt, compared to $56,000 in the same period in 2005. Additionally, in the
six months ended June 30, 2006 and 2005, $68,000 and $42,000 was used for
capital lease obligations, respectively. Financing activities in the six months
ended June 30, 2006 also included proceeds from a minority equity investment in
our Japan subsidiary of $5.1 million. Financing activities in the six months
ended June 30, 2005 also included proceeds from long-term debt of $0.8 million
and the repurchase of common stock for treasury of $0.9 million.

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
financing 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.



                                       15
<PAGE>



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

CONTRACTUAL OBLIGATIONS

The following summarizes our contractual obligations at June 30, 2006, and the
effect those obligations are expected to have on our liquidity and cash flow in
future periods (in thousands).

<TABLE>
<CAPTION>

                                                             JULY 2006-     JULY 2007-      JULY 2009      JULY 2011 AND
                                                  TOTAL      JUNE 2007      JUNE 2009       JUNE 2011       THEREAFTER
                                                 -------     ----------     ----------      ---------      -------------
<S>                                             <C>             <C>             <C>            <C>            <C>
CONTRACTUAL OBLIGATIONS
Non-cancelable operating lease obligation        $10,951        $ 1,916        $ 4,066        $ 4,398           $    571
Capital lease obligations ...............            337            156            151             30                 --
License arrangements ....................          2,601            955          1,196            450                 --
Long-term debt ..........................            884            422            442             20                 --
Other long-term liabilities (1) .........            927            795            132             --                 --
                                                 -------     ----------     ----------      ---------      -------------
Total obligations .......................        $15,700        $ 4,244        $ 5,987        $ 4,898           $  571
                                                 -------     ----------     ----------      ---------      -------------
</TABLE>


(1) The amounts shown represent contractual obligations that had original
maturities beyond one year.

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, litigation 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


                                       16
<PAGE>


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 year ended December 31, 2005 filed with the
Securities and Exchange Commission. There have been no material changes to such
exposures during the second 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(R) 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(R) 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. Appellate briefing was completed on July 10, 2006.

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(TM) chemistry. The complaint was served on us in September 2005. Recently,
at the request of both parties, the Court rescheduled the trial date to April 7,
2008.

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 HPV patents for
one year.

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.



                                       17
<PAGE>



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. - None.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES - None.

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

     At the Annual Meeting of Stockholders held on June 13, 2006, the following
matters were submitted to a vote of security holders:

     1.   the election of Gordon Brunner and Lawrence Murphy to serve as
          directors with terms ending in 2009, and

     2.   the proposal to ratify the appointment of Grant Thornton LLP as
          independent registered public accounting firm for the fiscal year
          ending December 31, 2006.

The nominees for director were elected based upon the following votes:

                 DIRECTOR              VOTES FOR            VOTES WITHHELD

                 Gordon Brunner        38,952,991                1,090,383
                 Lawrence Murphy       39,106,052                  937,322


In addition to Mr. Brunner and Mr. Murphy, the term of office of each of the
following directors continued after the meeting: David A. Thompson, Kevin T.
Conroy, James Connelly, and Lionel Sterling.

The appointment of Grant Thornton LLP as the Company's independent auditors for
the fiscal year ending December 31, 2006 was ratified, as follows:


       VOTES FOR        VOTES AGAINST   VOTES ABSTAIN  BROKER NON-VOTES
       39,857,288       173,114         12,972               0

ITEM 5. OTHER INFORMATION. - None.


ITEM 6. EXHIBITS

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



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<PAGE>



                                   SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the
Registrant has duly caused this report to be signed on its behalf by the
undersigned, thereunto duly authorized.

                                       THIRD WAVE TECHNOLOGIES, INC.

Date: August 8, 2006                   /s/ Kevin T. Conroy
                                       -----------------------------------------
                                       Kevin T. Conroy, Chief Executive Officer

Date: August 8, 2006                   /s/ Maneesh K. Arora
                                       -----------------------------------------
                                       Maneesh K. Arora, Chief Financial Officer




                                       19
<PAGE>



                                  EXHIBIT INDEX

<TABLE>
<CAPTION>

   EXHIBIT
     NO.                           DESCRIPTION                                            INCORPORATED BY REFERENCE TO
-------------  ------------------------------------------------------------------  ----------------------------------------
<S>  <C>                                                                           <C>
     10.1      2000 Stock Plan, as amended                                         Exhibit 4.1 to Registrant's Registration
                                                                                   Statement on Form S-8 filed on June 6, 2006

     10.2      Form of Stock Option Agreement                                      Exhibit 4.2 to Registrant's Registration
                                                                                   Statement on Form S-8 filed on June 6, 2006

     10.3      Form of Restricted Stock Purchase Agreement                         Exhibit 4.3 to Registrant's Registration
                                                                                   Statement on Form S-8 filed on June 6, 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>




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