This book constitutes the refereed proceedings of the Second International Workshop on Medical Imaging and Augmented Reality, MIAR 2004, held in Beijing, China, in August 2004.The 41 revised full papers presented together with 4 invited papers were carefully reviewed and selected from 93 submissions. The papers are organized in topical sections on image processing, reconstruction, and coding; statistical and shape based segmentation; brain image analysis; cardiac modeling and segmentation; image registration; and surgical navigation and augmented reality.