The 6th International Conference on Medical Imaging and Augmented Reality, MIAR 2016, was held in Bern, Switzerland during August 2016. The aim of MIAR is to bring together researchers in computer vision, graphics, robotics, and medical imaging to present the state-of-the-art developments in this ever-growing research area in topics such as:Medical Image Formation, Analysis and InterpretationAugmented Reality, Visualization and SimulationComputer Assisted Interventional and Robotics, Surgical PlanningSystematic Extra- and Intra-corporeal Imaging ModalitiesGeneral Biological and Neuroscience Image Computing