Alzheimer's disease is the most common neurodegenerative disorder in the elderly. Amnestic mild cognitive impairment (MCI) is a relatively newly defined clinical entity that requires memory decline while activities of daily living remain intact. Most amnestic MCI patients develop Alzheimer's disease. Using an innovative surface-based hippocampal analytic technique we analysed the structural magnetic resonance hippocampal data of 31 amnestic MCI and 34 Alzheimer's disease subjects. We tested the hypothesis that Alzheimer's disease subjects have greater atrophy of the CA1, CA2 and CA3 hippocampal subfields relative to amnestic MCI subjects. 3D hippocampal maps localized the main group differences to the CA1 region bilaterally and the CA2 and CA3 region on the left [corrected] (right [corrected] P = 0.0024, left [corrected] P = 0.0002, both corrected for multiple comparisons). Age, race, gender, education and Mini-Mental State Examination were significant predictors of hippocampal volume. Hippocampal volume was a significant predictor of clinical diagnosis. Our study suggests that as Alzheimer's disease progresses, subregional hippocampal atrophy spreads in a pattern that follows the known trajectory of neurofibrillary tangle dissemination. Novel hippocampal analytic techniques that can track the spread of hippocampal pathology in 3D with such precision are a promising research tool.