This book constitutes the refereed proceedings of the Third International Workshop on Multimodal Brain Image Analysis, MBIA 2013, held in Nagoya, Japan, on September 22, 2013 in conjunction with the 16th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI. The 24 revised full papers presented were carefully reviewed and selected from 35 submissions. The papers are organized in topical sections on analysis, methodologies, algorithms, software systems, validation approaches, benchmark datasets, neuroscience and clinical applications.