Exhibit 31.1I, Joseph D. Keegan, Ph.D., certify that:1. I have reviewed this quarterly report on Form 10-Q of Molecular DevicesCorporation;2. Based on my knowledge, this report does not contain any untruestatement of a material fact or omit to state a material fact necessary to makethe statements made, in light of the circumstances under which such statementswere made, not misleading with respect to the period covered by thisreport;3. Based on my knowledge, the financial statements, and otherfinancial information included in this report, fairly present in allmaterial respects the financial condition, results of operationsand cash flows of the registrant as of, and for, the periods presented in thisreport;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)) forthe registrant and have:a) Designed such disclosure controls and procedures, or caused suchdisclosure controls and procedures to be designed under oursupervision, to ensure that material information relating to theregistrant, including its consolidated subsidiaries, is made known tous by others within those entities, particularly during the period inwhich this report is being prepared;b) Designed such internal control over financial reporting, or causedsuch internal control over financial reporting to be designed under oursupervision, to provide reasonable assurance regarding the reliabilityof financial reporting and the preparation of financial statementsfor external purposes in accordance with generally accepted accountingprinciples;c) Evaluated the effectiveness of the registrant’s disclosure controlsand procedures and presented in this report our conclusionsabout the effectiveness of the disclosure controls and procedures, asof the end of the period covered by this report based on suchevaluation; andd) Disclosed in this report any change in the registrant’sinternal control over financial reporting that occurred during theregistrant’s most recent fiscal quarter (the registrant’s fourthfiscal quarter in the case of an annual report) that has materiallyaffected, or is reasonably likely to materially affect, theregistrant’s internal control over financial reporting.5. The registrant’s other certifying officer(s) and I have disclosed, basedon our most recent evaluation of internal control over financial reporting, tothe registrant’s auditors and the audit committee of registrant’s board ofdirectors (or persons performing the equivalent functions):a) All significant deficiencies and material weaknesses in the designor operation of internal control over financial reporting which arereasonably likely to adversely affect the registrant’s ability torecord, process, summarize and report financial information; andb) Any fraud, whether or not material, that involves management orother employees who have a significant role in the registrant’sinternal control over financial reporting.Date: August 5, 2005   /s/ Joseph D. Keegan     Joseph D. Keegan, Ph.D.  President and Chief Executive Officer