The 2013 workshop in medical computer vision (MCV) took place in Nagoya, Japan in connection with MICCAI (Medical Image Computing for Computer Assisted Intervention). It is the third MICCAI MCV workshop after 2011 and 2012 also related to a similar workshop held at CVPR (Computer Vision and Pattern Recognition) in 2012. The workshop aims at exploring the use of modern computer vision technology in tasks such as automatic segmentation and registration, localisation of anatomical features and detection of anomalies. It emphasises questions of harvesting, organising and learning from large-scale medical imaging data sets and general-purpose automatic understanding of medical images. We are especially interested in modern, scalable and efficient algorithms which generalise well to previously unseen images. The strong participation of over 70 persons in the workshop shows the importance and timeliness of medical computer vision as a research field. This overview article describes the papers presented in the workshop as either oral presentations or short presentations and posters. It also describes the invited talks and the results of the VISCERAL session in the workshop on the use of big data in medical imaging.