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                                                                    EXHIBIT 10.6

                         THIRD WAVE TECHNOLOGIES, INC.
                      1999 NONQUALIFIED STOCK OPTION PLAN

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     1.   PURPOSE. The purpose of the THIRD WAVE TECHNOLOGIES, INC. 1999
NONQUALIFIED STOCK OPTION PLAN (the "Plan") is to encourage certain employees,
and certain members of, and advisors to, the Board of Directors of the
Corporation of Third Wave Technologies, Inc. (the "Corporation") to acquire to
increase their stock ownership in the Corporation, to provide and incentive to
such individuals to promote the financial success of the Corporation, and to
enable the Corporation to attract and retain the personnel necessary for
continued growth and profitability.

     2.   EFFECTIVE DATE AND TERM OF PLAN. The Plan shall become effective as
of October 7, 1999, and shall continue in effect for an indefinite period
thereafter subject to termination as provided in Paragraph 17.

     3.   STOCK SUBJECT TO PLAN. Only common stock, with $1.00 par value per
share, of the Corporation ("Common Stock") may be issued pursuant to options
granted under this Plan. The maximum number of shares of Common Stock that may
be issued pursuant to the exercise of options granted under the Plan
("Options") is Four Hundred Fifty-nine (459) shares of the Corporation's common
stock less the number of shares of Common Stock that may be issued pursuant to
the Third Wave Technologies, Inc. 1999 Incentive Stock Option Plan effective as
of the date of this Plan, subject to any adjustments provided in Paragraph 16.
If any Options expire or terminate for any reason without having been exercised
in full, the unpurchased shares subject thereto shall again be available for
further grants under the Plan.

     4.   ADMINISTRATION. The Plan shall be administered by the committee
described in Paragraph 5 (the "Committee"). Subject to the express provisions of
the Plan, the Committee shall have complete authority in its discretion to
determine those employees, directors, and advisors ("Participants") to whom
Options shall be granted, the Option Price, the Option Periods and the number of
shares subject to each Option. Subject to the express provisions of the Plan,
the Committee shall also have the authority in its discretion to prescribe the
time or times at which Options may be exercised, the limitations upon the
exercise of Options (including limitations effective upon death, disability, or
termination of employment of any Participant) and the restrictions, if any, to
be imposed upon the transferability of shares acquired upon exercise of Options.
In making such determinations, the Committee may take into account the nature of
the services rendered by the respective Participants, their present and
potential contributions to the success of the Corporation, and such other
factors as the Committee in its discretion shall deem relevant. Subject to the
express provisions of the Plan, the Committee shall also have complete authority
to interpret the Plan, to prescribe, amend and rescind rules and regulations
relating to the Plan, to determine the terms and provisions of the respective
Option Agreements described in Paragraph 13 (which need not be identical), to
determine whether the shares delivered upon exercise of Options will be treasury
shares or will be authorized but previously unissued shares, and to make all
other determinations necessary or advisable for the administration of the Plan.
The Committee's determination on the matters referred to in this Paragraph shall
be conclusive.

     5.   COMMITTEE. The Committee shall consist of not less than two members
of the Board of Directors, each of whom shall be (i) a "non-employee director"
as that term is defined in Rule 16b-3 promulgated under the Securities and
Exchange Act of 1934, as amended (the "Exchange Act"), and (ii) an "outside
director" within the meaning of Section 162(m) of the Internal Revenue Code of
1986, as amended (the "Code"). The Committee shall be appointed from time to
time by the Board of Directors, which may from time to time appoint members of
the Committee in substitution for members previously appointed and may fill
vacancies, however caused, in the Committee. A majority of its members shall
constitute a quorum. All determinations of the


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Committee shall be made by a majority of its members. Any decision or
determination reduced to writing and signed by all of the members shall be
fully as effective as if it had been made by a majority vote at a meeting duly
called and held. The Committee may hold meetings by use of conference telephone
or similar communications equipment by which all persons participating in the
meeting can hear each other.

     6. ELIGIBILITY. Options may be granted under the Plan to those employees,
directors and advisors designated as eligible to participate by the Committee.
Such designations shall be subject to the approval of the Board of Directors.
The Committee shall inform each individual so designated of his or her
eligibility to participate in the Plan. Participation in the Plan shall be
entirely voluntary. Members of the Committee shall not, while serving as
members of the Committee, be eligible to receive Options.

     7. STOCK OPTIONS. The number of shares subject to any Options granted
under this Plan shall be established by the Committee. The Committee shall
notify each Participant of the number of shares subject to the Option granted
to the Participant.

     8. OPTION PRICE. The Option Price per share shall be determined by the
Committee at the time each Option is granted. The Committee shall notify each
Participant of the Option Price per share of the stock subject to the Option
granted to the Participant.

     9. OPTION PERIODS. The term of each Option shall be for a period
determined by the Committee (the "Option Period"). An Option shall be
considered granted on the date the Committee acts to grant the Option, or such
other date as the Committee shall specify. The Committee shall inform each
Participant of the Option Period applicable to the Option granted to the
Participant. Each Option shall be subject to earlier termination as described
under Paragraph 17.

     10. EXERCISE OF OPTIONS. Subject to the restrictions in Paragraph 12 and
in the agreement referred to in Paragraph 13, each Option may be exercised at
any time during the Option Period for such Option by written notice delivered
to an officer of the Corporation, stating the number of shares with respect to
which the Option is being exercised. In no event shall the Corporation be
required to transfer fractional shares to a Participant.

     11. PAYMENT FOR SHARES. Within five (5) business days following the date
of exercise, the Participant shall make full payment of the Option Price
either: (i) in cash; (ii) with the consent of the Committee, by tendering
previously acquired shares of Common Stock which on the date of tender (A) have
a fair market value, as determined by the Committee equal to the aggregate
option price and (B) in the case of shares required by previous exercise of an
option, have been owned by the Participant for more than six months; or (iii)
any combination of (i) or (ii). Shares of Common Stock tendered shall be duly
endorsed in blank or accompanied by stock powers duly endorsed in blank. Upon
receipt of the payment of the entire Option Price for the shares so purchased,
certificates for such shares shall be delivered to the Participant. Such
certificates shall bear a legend on the reverse side reflecting the transfer
restrictions described in Paragraph 12.

     12. TRANSFER RESTRICTIONS. Shares of common stock purchased under the Plan
are governed by, and may not be sold or otherwise disposed of except in
compliance with (i) the Corporation's Bylaws and (ii) the registration
requirements of the Securities Act of 1933 and any applicable state securities
laws (unless such transaction is, in the opinion of counsel for the
Corporation, exempt from registration under such Act and laws). The
transferability of such shares shall be subject to the restrictions contained
in the Shareholder Agreement in the form attached hereto and made part hereof
as Exhibit A, which the Participant agrees to: execute upon the exercise of an
option; and take such other action as may be required by the Board of Directors
from time to time.


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     13.  OPTION AGREEMENTS.  Options granted pursuant to the Plan shall be
evidenced by a stock option agreement in the form attached hereto as Exhibit B,
or as otherwise may be required by the Committee from time to time, except that
in the case of a "Key Employee," as defined in Paragraph 15 below, the stock
option agreement will include such different or additional terms as are
required by Paragraph 15 below and the 1999 Investment Agreement, also as
defined in Paragraph 15 below.

     14.  TERMINATION OF OPTION.  Except as hereinafter provided, no Option may
be exercised later than three months after a Participant terminates his or her
employment, or services with the Corporation or its Subsidiaries, as the case
may be. If such termination results from the deliberate, willful or gross
misconduct of a Participant, then the Option may not be exercised and all of
the Participant's rights in the Option shall be forfeited upon termination. If
such termination results from the disability of a Participant within the
meaning of Section 22(e)(3) of the Code, any Option may be exercised at any
time within twelve months after such termination of employment, but in no event
beyond the Option Period. If such termination results from death of a
Participant, the personal representative of the Participant's estate, or a
person who by bequest, inheritance, or otherwise by reason of the Participant's
death, acquired the right to exercise the Option, may exercise any Option at
any time within three years after the death of such Participant, but in no
event beyond the Option Period. The Committee may impose additional
restrictions upon the exercise of Options after termination of employment or
services with the Corporation, including prohibition of such exercise.

     15.  CHANGE IN CONTROL.  In the case of a Key Employee, as the term is
defined in the Investment agreement dated as of July 21, 1999, by and among the
Corporation and Schroeder Ventures International Life Sciences Fund II et al
(the "1999 Investment Agreement"), the terms of his or her stock option
agreement shall further provide that in the event of an Adjustment to the
Applicable Conversion Value pursuant to Sections 5.5(a) or 5.5(e) of Article
III of the Corporation's Amended and Restated Articles of Incorporation (the
"Articles"), but not an Adjustment to the Applicable Conversion Value as a
result of a Below Projection Liquidity Event pursuant to section 5.5(h) of
Article III of the Articles, all rights of the holder of the Option shall
automatically terminate and holder of the Option shall automatically forfeit
such Option to the Corporation and, to the extent such Option has been
previously exercised, the holder shall automatically forfeit any such shares
received upon such prior exercise, provided that in such event the Corporation
shall reimburse the holder thereof for all consideration previously paid to the
Corporation upon the exercise of such Option.

     16.  NONTRANSFERABILITY OF OPTIONS.  Options under the Plan are not
transferable by a Participant other than by will or the laws of descent or
distribution, and may be exercised during the lifetime of a Participant only
by the Participant.

     17.  ADJUSTMENT OF NUMBER OF SHARES.  In the event of any change in the
number or kind of shares of outstanding common stock of the Corporation by
reason of stock dividends, recapitalizations, reorganizations, mergers,
consolidations, split-ups, combinations or exchanges of shares and the like,
the Committee shall, consistent with such change, appropriately adjust the
number and kind of shares which thereafter may be optioned and sold under the
Plan, the number and kind of shares under Option in outstanding Option
Agreements, and the purchase price per share thereof. The determination of the
Committee as any such adjustment shall be final and conclusive. No adjustment
or substitution provided for in this paragraph shall require the Corporation in
any Stock Option Agreement to sell a fractional share, and the total
substitution or adjustment with respect to each Option Agreement shall be
limited accordingly.

     18.  AMENDMENT, SUSPENSION, OR TERMINATION.  The Board of Directors may
from time to time amend, suspend or terminate the Plan in such respects as the
Board may deem advisable. No amendment shall, without the Participant's
consent, alter or impair any of the rights or obligations under any Option
therefore granted to the Participant.

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     19.  APPLICABLE LAW.  The Plan shall, to the extent not inconsistent with
applicable federal law, be construed under the laws of the State of Wisconsin.

     Dated as of this 7th day of October, 1999.


                                        THIRD WAVE TECHNOLOGIES, INC.


                                        BY:
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                                            Lance Fors, President and
                                            Chief Executive Officer


                                        ATTEST:
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                                                David C. Sneider,
                                                Chief Financial Officer





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