This book constitutes the refereed proceedings of the Second International Workshop on Patch-Based Techniques in Medical Images, Patch-MI 2016, which was held in conjunction with MICCAI 2016, in Athens, Greece, in October 2016.The 17 regular papers presented in this volume were carefully reviewed and selected from 25 submissions. The main aim of the Patch-MI 2016 workshop is to promote methodological advances within the medical imaging field, with various applications in image segmentation, image denoising, image super-resolution, computer-aided diagnosis, image registration, abnormality detection, and image synthesis.