OBJECTIVE The development of a computerized system for protocol management, dispensing, inventory accountability, and billing by the investigational drug service (IDS) of a university health system is described. CONCLUSIONS After an unsuccessful search for a commercial system that would accommodate the variation among investigational protocols and meet regulatory requirements, the IDS worked with the health-system pharmacy's information technology staff and informatics pharmacists to develop its own system. The informatics pharmacists observed work-flow and information capture in the IDS and identified opportunities for improved efficiency with an automated system. An iterative build-test-design process was used to provide the flexibility needed for individual protocols. The intent was to design a system that would support most IDS processes, using components that would allow automated backup and redundancies. A browser-based system was chosen to allow remote access. Servers, bar-code scanners, and printers were integrated into the final system design. Initial implementation involved 10 investigational protocols chosen on the basis of dispensing volume and complexity of study design. Other protocols were added over a two-year period; all studies whose drugs were dispensed from the IDS were added, followed by those for which the drugs were dispensed from decentralized pharmacy areas. The IDS briefly used temporary staff to free pharmacist and technician time for system implementation. Decentralized pharmacy areas that rarely dispense investigational drugs continue to use manual processes, with subsequent data transcription into the system. Through the university's technology transfer division, the system was licensed by an external company for sale to other IDSs. CONCLUSIONS The WebIDS system has improved daily operations, enhanced safety and efficiency, and helped meet regulatory requirements for investigational drugs.