Medical image fusion is the process of registering and combining multiple images from single or multi-ple imaging modalities. By this method, the randomness and redundancy of medical images are reduced and the image quality is improved for diagnosis and treatment assessment of medical problems. The first image fusion method exclusively used in dentistry was introduced in 1994. It was based on the radiographs additive to three primary colors, i.e., red, blue and green to show the differences between sequential radiographs over time. Using this algorithm, the eruption pattern of auto transplanted tooth, alveolar bone gain/loss after periodontal surgery, and the progression of orthodontic treatment were successfully evaluated. With the advent of cone beam computed tomography, more and more studies have focused on the three dimensional evaluation of facial profile, facial skeleton and dentition from orthodontic therapy and orthognathic treatment by the use of image fusion, and demonstrated promising results. Nowadays, image fusion is also used for the three dimensional evaluation of disorders related to temopomadibular joint and the neoplasm in the head and neck.