Exhibit 31.1CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER PURSUANT TOSECTION 302 OF THE SARBANES-OXLEY ACT OF 2002I, Henry L. Nordhoff, certify that:1. I have reviewed this quarterly report on Form 10-Q of Gen-Probe Incorporated;2. Based on my knowledge, this report does not contain any untrue statement of a material fact oromit to state a material fact necessary to make the statements made, in light of the circumstancesunder which such statements were made, not misleading with respect to the period covered by thisreport;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 of operationsand cash flows of the registrant as of, and for, the periods presented in this report;4. The registrant’s other certifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) andinternal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and5(d)-15(f)) for the registrant and we have: (a) Designed such disclosure controls and procedures, or caused such disclosurecontrols and procedures to be designed under our supervision, to ensure that materialinformation relating to the registrant, including its consolidated subsidiaries, ismade known to us by others within those entities, particularly during the period inwhich this report is being prepared;  (b) Designed such internal control over financial reporting, or caused suchinternal control over financial reporting to be designed under our supervision, toprovide reasonable assurance regarding the reliability of financial reporting and thepreparation of financial statements for external purposes in accordance with generallyaccepted accounting principles;  (c) Evaluated the effectiveness of the registrant’s disclosure controls andprocedures and presented in this report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by this reportbased on such evaluation; and  (d) Disclosed in this report any change in the registrant’s internal control overfinancial reporting that occurred during the registrant’s most recent fiscal quarter(the registrant’s fourth fiscal quarter in the case of an annual report) that hasmaterially affected, or is reasonably likely to materially affect, the registrant’sinternal control over financial reporting; and5. 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 the auditcommittee of the registrant’s board of directors (or persons performing the equivalent functions): (a) All significant deficiencies and material weaknesses in the design oroperation of internal control over financial reporting which are reasonably likely toadversely affect the registrant’s ability to record, process, summarize and reportfinancial information; and  (b) Any fraud, whether or not material, that involves management or otheremployees who have a significant role in the registrant’s internal control overfinancial reporting.     DATE: May 5, 2006 By: /s/ Henry L. Nordhoff         Henry L. Nordhoff    Chairman, President and Chief ExecutiveOfficer