AIM:To investigate ischemia reperfusion (I/R)-induced proteomic changes in rat skeletal muscle. METHODS: Healthy male Wistar rats were randomly divided into two groups as follows (n=6): sham group and I/R group. I/R of right hind limb was induced by 4 h ischemia followed by 24 h reperfusion. The 2-DE was applied to separate the proteins extracted from skeletal muscle tissue at the end of experiment, followed by Coomassie Brillant blue R-250 staining. Computer image analysis was used to determine the differential expression of proteins between the two groups, and 7 protein spots expressed differentially were picked out and subjected to in-gel digest and MALDI-TOP for identification. RESULTS: 354?13 proteins were detected and the match rate was (78.7?1.4)%. 10 proteins displayed significant changes after I/R, of which, 6 proteins increased and 3 proteins decreased in expression. Moreover, 2 spots in I/R group were observed, only 1 spots of which in control. 5 proteins were identified after mass spectrometry. Mitochondrial aldehyde dehydrogenase (ALDH) precursor, heat shock 27 kD protein (HSP27), an unnamed protein product (increased in I/R group), ?-actin (decreased in I/R group), and nuclear transport factor 2 (NTF-2) W7a mutant were found in I/R group. CONCLUSION: I/R injury induced differential proteomic changes in rat skeletal muscle. ALDH, ?-actin and HSP27 expression, and NTF-2 mutation are involved in I/R injury.