It is widely accepted that intersexual differences occur in cognitive domains, e.g., in spatial learning and memory. The hippocampus plays important roles in the consolidation of information from short-term memory to long-term memory and spatial navigation. However, it still remains unknown whether the hippocampal proteomic profiling differs between males and females. In this study, we investigated the intersexual differences in protein expression of hippocampi using the two-dimensional electrophoresis analysis. In all, 33 differentially expressed proteins were characterized by matrix-assisted laser desorption and ionization time-of-flight mass spectrometry and validated by Western-blotting analysis. In line with Western-blotting validation, the proteomic identification revealed the overexpression of glial fibrillary acidic protein in female rats' hippocampi, and the overexpression of both creatine kinase B-type and DRP-2 in male rats' hippocampi. The intersexual differences in hippocampal proteomic profiling are probably closely related to those in spatial learning and memory abilities. Anat Rec, 296:462–469, 2013. © 2013 Wiley Periodicals, Inc.