Exhibit 31.1I, Joseph D. Keegan, Ph.D., certify that:1. I havereviewed this quarterly report on Form 10-Q of Molecular Devices Corporation;2. Based on my knowledge, this report does not contain any untrue statement of amaterial fact or omit to state a material fact necessary to make the statementsmade, in light of the circumstances under which such statements were made, notmisleading with respect to the period covered by this report;3. Based on my knowledge, the financial statements, and other financialinformation included in this report, fairly present in all material respects thefinancial condition, results of operations and cash flows of the registrant asof, and for, the periods presented in this report;4. The registrant’s other certifying officer(s) and I are responsible forestablishing and maintaining disclosure controls and procedures (as defined inExchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financialreporting (as defined in Exchange Act Rules 13a — 15(f) and 15d — 15(f)) for theregistrant and have:a) designed such disclosure controls and procedures, or caused suchdisclosure controls and procedures to be designed under our supervision,to ensure that material information relating to the registrant, includingits consolidated subsidiaries, is made known to us by others within thoseentities, particularly during the period in which this report is beingprepared;b) designed such internal control over financial reporting, or caused suchinternal control over financial reporting to be designed under oursupervision, to provide reasonable assurance regarding the reliability offinancial reporting and the preparation of financial statements forexternal purposes in accordance with generally accepted accountingprinciples;c) evaluated the effectiveness of the registrant’s disclosure controls andprocedures and presented in this report our conclusions about theeffectiveness of the disclosure controls and procedures, as of the end ofthe period covered by this report based on such evaluation; andd) disclosed in this report any change in the registrant’s internalcontrol over financial reporting that occurred during the registrant’smost recent fiscal quarter (the registrant’s fourth fiscal quarter in thecase of an annual report) that has materially affected, or is reasonablylikely to materially affect, the registrant’s internal control overfinancial reporting; and5. The registrant’s other certifying officer(s) and I have disclosed, based onour most recent evaluation of internal control over financial reporting, to theregistrant’s auditors and the audit committee of 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 arereasonably likely to adversely affect the registrant’s ability to record,process, summarize and report financial information; andb) any fraud, whether or not material, that involves management or otheremployees who have a significant role in the registrant’s internal controlover financial reporting.Date: May 10, 2006   /s/ Joseph D. Keegan     Joseph D. Keegan, Ph.D.  President and Chief Executive Officer