This book constitutes the refereed proceedings of the Second International Workshop on Multimodal Brain Image Analysis, held in conjunction with MICCAI 2012, in Nice, France, in October 2012. The 19 revised full papers presented were carefully reviewed and selected from numerous submissions. The objective of this workshop is to forward the state of the art in analysis methodologies, algorithms, software systems, validation approaches, benchmark datasets, neuroscience, and clinical applications.