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This book constitutes the thoroughly refereed post-workshop proceedings of the Third International Workshop on Medical Computer Vision, MCV 2013, held in Nagoya, Japan, in September 2013 in conjunction with the 16th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2013. The 7 revised full papers and 12 poster papers presented were selected from 25 submissions. They have been organized in topical sections on registration and visualization, segmentation, detection and localization, and features and retrieval. In addition, the volume contains two invited papers describing segmentation task and data set of the VISCERAL benchmark challenge.