MRI-based volumetric assessment of brain structure has been widely employed in the studies of AD, MCI, and healthy aging and consistent findings of the studies include volume loss in the hippocampus and entorhinal cortex. In this study, we assessed surface shape differences of the hippocampus, which reflect regional volume changes, through automated hippocampal segmentation in subjects of healthy aging, MCI, and AD. Same number of healthy control (n = 25), MCI subjects (n = 25), and patients with probable AD (n = 25) were included. The automated hippocampal segmentation method with group specific template was used for reconstruction of three dimensional hippocampal shapes in each subject. In each subject, the locations of the hippocampal surface were registered on an age-matched neuroanatomical template and variations in hippocampal diameter were calculated. To validate the accuracy of the automated methods, one reader manually outlined the boundary of the hippocampus and the results were compared with those of automated methods. Significant surface shape differences were observed between normal aging and AD in the lateral zone of the body of both hippocampi and the inferior-medial zone of the left hippocampal body, which are proximal to the cornu ammonis (CA)1 subfield and the subiculum. Between amnestic MCI and AD, there were also significant shape differences in the lateral and inferior-medial zones of the left hippocampal body and lateral surface of the hippocampal tail of the right hippocampus. However, a comparison of amnestic MCI and normal control did not reveal significant differences. In AD, atrophic changes appear in the hippocampus; however, this is not a unique finding of AD without specification of sub-regions and can also be seen in other types of dementia, MCI, and healthy aging. In this study, hippocampal surface deformation was most pronounced in areas covering the CA1 subfield and the subiculum in AD compared to normal control and MCI. The automated surface analysis used in this study is easier to use than the manual-drawing method and displays specific deformational changes of the hippocampus in AD, which could be a useful tool for group-level studies.