EXHIBIT 31.1CERTIFICATIONI, Kevin T. Conroy, Chief Executive Officer of Third Wave Technologies, Inc. (the “registrant”),certify that:1. I have reviewed this Quarterly Report on Form 10-Q (the “Report”) of the registrant; 2. Based on my knowledge, this Report does not contain any untrue statement of a material factor omit to state a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading with respect to the periodcovered by this Report; 3. Based on my knowledge, the financial statements, and other financial information included inthis Report, fairly present in all material respects the financial condition, results ofoperations and cash flows of the registrant as of, and for, the periods presented in theReport; 4. The registrant’s other certifying officer and I are responsible for establishing andmaintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and15d-15(e) and internal control over financial reporting as defined in Exchange Act Rule13a-15(f) and 15d-15(f)) for the registrant and have: (a) designed such disclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that material informationrelating to the registrant, including its consolidated subsidiaries, is made known to us byothers within those entities, particularly during the period in which this Report is beingprepared;  (b) designed such internal control over financial reporting, or caused such internal controlover financial reporting to be designed under our supervision, to provide reasonableassurance regarding the reliability of financial reporting and the preparation of financialstatements for external purposes in accordance with generally accepted accountingprinciples;  (c) evaluated the effectiveness of the registrant’s disclosure controls and procedures andpresented in the Report our conclusions about the effectiveness of the disclosure controlsand procedures, as of the end of the period covered by the Report, based on such evaluation;and  (d) disclosed in the Report any change in the registrant’s internal control over financialreporting that occurred during the registrant’s most recent fiscal quarter that hasmaterially affected, or is reasonably likely to materially affect, the registrant’s internalcontrol over financial reporting; and,5. The registrant’s other certifying officer and I have disclosed, based on our most recentevaluation of internal control over financial reporting, to the registrant’s auditors and theaudit committee of registrant’s board of directors (or persons performing the equivalentfunctions): (a) all significant deficiencies and material weaknesses in the design or operation ofinternal control over financial reporting which are reasonably likely to adversely affectthe registrant’s ability to record, process, summarize and report financial data; and  (b) any fraud, whether or not material, that involves management or other employees who havea significant role in the registrant’s internal control over financial reporting.Date: November 1, 2007                                             /s/ Kevin T. Conroy   Kevin T. Conroy,   Chief Executive Officer  
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