This book constitutes the refereed proceedings of the 12th Conference on Artificial Intelligence in Medicine in Europe, AIME 2009, held in Verona, Italy in July 2009. The 24 revised long papers and 36 revised short papers presented together with 2 invited talks were carefully reviewed and selected from 140 submissions. The papers are organized in topical sections on agent-based systems, temporal data mining, machine learning and knowledge discovery, text mining, natural language processing and generation, ontologies, decision support systems, applications of AI-based image processing techniques, protocols and guidelines, as well as workflow systems.