This book constitutes the refereed proceedings of the 16th Conference on Artificial Intelligence in Medicine, AIME 2017, held in Vienna, Austria, in June 2017.The 21 revised full and 23 short papers presented were carefully reviewed and selected from 113 submissions. The papers are organized in the following topical sections: ontologies and knowledge representation; Bayesian methods; temporal methods; natural language processing; health care processes; and machine learning, and a section with demo papers.