In this study, we aimed to (1) propose landmarks for the hippocampus in a rat brain using an experimental study and (2) investigate hippocampus shape changes in a rat brain with epilepsy using the statistical shape analysis method. We have used the statistical shape analysis method to illustrate hippocampal shape deformation due to epilepsy. Statistical shape analysis is of increasing interest to the neuroimaging community because of its potential for locating morphological changes. Nineteen rat brains (ten healthy and nine epileptic) with hematoxylin and eosin images of the hippocampus were used. The results strongly indicated that the normalized hippocampal shape of the epileptic group was different from the nonepileptic group; deformation was seen most significantly in the medial regions of the cornu ammonis (CA1 and CA3) of the hippocampus. In conclusion, our landmark-based methodology detected regional differences in the hippocampus in epilepsy. This study may serve as an initial reference for future studies on shape alteration of the hippocampus associated with certain medical conditions.