The Third International Workshop on Medical Imaging and Augmented Reality, MIAR 2006, was held in Shanghai, China at the Regal International East Asia Hotel during August 17-18, 2006. The goal of MIAR 2006 was to bring together researchers in medical image computing and intervention to present the state-of-the-art devel- ments in this ever-growing research area. The meeting consisted of a single track of oral/poster presentations, with each session led by an invited lecture from our dist- guished international faculty members. For MIAR 2006, we received 87 full subm- sions, which were subsequently reviewed by up to 5 reviewers, resulting in the acc- tance of 45 full papers included in this volume. For this workshop, we also included four papers from the invited speakers covering shape modeling, fMRI analysis, and study of cerebral connectivity and plasticity. Running such a workshop requires dedication, and we appreciate the commitment of the MIAR 2006 Programme Committee and reviewers who worked to a tight de- line in putting together this workshop. We would also like to thank members of the local Organizing Committee, who have been working so hard behind the scenes to make MIAR 2006 a great success. It was our great pleasure to welcome this year's MIAR attendees to Shanghai, which is the largest base of Chinese industrial technology, an important seaport and China's largest commercial and financial center.