The hippocampus exhibits regional differences in vulnerability to ischemia, wherein pyramidal cells in the CA1 region are vulnerable to ischemia while pyramidal cells in the CA3 region and granule cells in the dentate gyrus (DG) region are relatively ischemia resistant. However, pyramidal cells in the CA1 region reportedly exhibit ischemic tolerance following exposure to a brief non-lethal period of ischemia known as ischemic preconditioning. In this study, we used proteomic analysis to examine the difference in protein expression between naïve rat CA1 and CA3/DG regions, as well as the altered protein expression in the CA1 region after 3min of ischemic preconditioning. Proteomic analysis identified ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCH-L1), glutathione S-transferase μ5 (GSTμ5), glutamine synthetase (GS), and dynamin-1 as proteins with differential expression levels in naïve CA1 and CA3/DG regions. The difference in expression levels of GSTμ5 and GS between these two regions was further confirmed by western blot. Our analysis also identified aconitase2, α-tubulin, protein-l-isoaspartate O-methiltransferase (PIMT), and voltage-dependent anion channel 1 (VDCA1) as proteins with down-regulated expression levels in the CA1 region following 3min ischemic preconditioning. The decrease in the expression of aconitase2 was also confirmed by western blot and immunohistochemical staining. The present results suggest that GSTμ5 and GS may be associated with ischemia-resistance in the CA3/DG region and that aconitase2 may play a part in the ischemic tolerance in the CA1 region.