Here are the refereed proceedings of the Third International Workshop on Medical Imaging and Augmented Reality, MIAR 2006, held in Shanghai, China, August 2006. The book presents 45 revised full papers together with 4 invited papers. The papers are organized in topical sections on shape modeling and morphometry, patient specific modeling and quantification, surgical simulation and skills assessment, surgical guidance and navigation, image registration, PET image reconstruction, and image segmentation.