Intestinal ischemia/reperfusion (I/R) injury is a critical condition associated with high morbidity and mortality. Our previous study showed that ischemic postconditioning (IPo) protects the intestinal mucosa from I/R injury. However, the precise molecular mechanisms of this event remain poorly elucidated. The aim of this study was to investigate the differentially expressed proteins of intestinal mucosa after intestinal I/R with or without IPo, and to explore the potential mechanisms of intestinal I/R injury and the protective effect of IPo in relation to the differential proteins.Intestinal I/R injury was established by occluding the superior mesenteric artery (SMA) for 60 min followed by 60 min reperfusion. The rats were randomly allocated into one of three groups based upon the intervention (n = 8); sham : sham surgical preparation including isolation of the SMA without occlusion was performed; injury: there was no intervention either before or after SMA occlusion; IPo: three cycles of 30 s reperfusion-30 s reocclusion were imposed immediately upon reperfusion. A comparative proteomics approach with two-dimensional gel electrophoresis was used to isolate proteins in intestinal mucosa, the expression of which were regulated by I/R injury post-treated with or without IPo. The differentially displayed proteins were identified through matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS).Image analysis revealed that an average of 1300 protein spots were detected on each gel; 16 and 9 proteins showing more than 1.5-fold difference were identified between the Sham versus Injury group and injury group versus IPo group, respectively. The identified proteins were functionally involved in the cellular processes of energy metabolism, anti-oxidation, and anti-apoptosis.This study provided new clues for understanding the mechanisms of IPo against intestinal I/R injury.