Background The reporting of serious adverse events is a requirement when conducting a clinical trial involving human subjects, necessary for the protection of the participants. The reporting process is a multi-step procedure, involving a number of individuals from initiation to final review, and must be completed in a timely fashion. Purpose The purpose of this project was to automate the adverse event reporting process, replacing paper-based processes with computer-based processes, so that personnel effort and time required for serious adverse event reporting was reduced, and the monitoring of reporting performance and adverse event characteristics was facilitated. Methods Use case analysis was employed to understand the reporting workflow and generate software requirements. The automation of the workflow was then implemented, employing computer databases, web-based forms, electronic signatures, and email communication. Results In the initial year (2007) of full deployment, 588 SAE reports were processed by the automated system, eSAEy (TM). The median time from initiation to Principal Investigator electronic signature was < 2 days (mean 7 perpendicular to 0.7 days). This was a significant reduction from the prior paper-based system, which had a median time for signature of 24 days (mean of 45 +/- 5.7 days). With eSAEy (TM), reports on adverse event characteristics (type, grade, etc.) were easily obtained and had consistent values based on standard terminologies. Limitation The automated system described was designed specifically for the workflow at Thomas Jefferson University. While the methodology for system design, and the system requirements derived from common clinical trials adverse reporting procedures are applicable in general, specific workflow details may not be relevant at other institutions. Conclusion The system facilitated analysis of individual investigator reporting performance, as well as the aggregation and analysis of the nature of reported adverse events. Clinical Trials 2009; 6: 446-454. http://ctj.sagepub.com