Objective To investigate the effect of S-adenosylmethionine (SAM) on mitochondrial injury that was induced by ischemia-reperfusion in rat liver. Methods Fifty-four rats were randomly divided equally into 3 groups: control group, ischemia-reperfusion group (I/R group), and SAM-treated group (SAM group). Hepatic ischemia had been only lasted for 30 min by obstructing the blood stream of hepatic portal vena (the portal vena was only separated but not obstructed in control group). The rats of SAM group received SAM intraperitoneally 2 h prior to ischemia. Blood samples of each group were collected from the inferior cava vena at 0, 1 and 6 h after reperfusion and the serum levels of AST and ALT were detected. Mitochondrial super oxidedismutase (SOD), malondialdehyde (MDA), adenosine triphosphate (ATP) and energy charge (EC) in samples of liver tissue were detected, and the mitochondrial ultrastructure was observed with electronmicroscope. Results The serum levels of AST, ALT and mitochondrial MDA at 0, 1 and 6 h after reperfusion in the I/R group were significantly higher than those in the control group, whereas the levels of mitochondrial SOD, ATP and EC were significantly lower than those in the control group (P＜0.01). Except the value of 0 h, when it comes to SAM group, the levels of AST, ALT and mitochondrial MDA were significantly lower (P＜0.05) and the levels of mitochondrial SOD, ATP and EC were significantly higher (P＜0.05, P＜0.01) than those in the I/R group, respectively. The mitochondrial ultrastructure was injured obviously in I/R group when compared with that in control group. The number of mitochondria decreased and the mitochondria swelled, making the crista became obscure and the density of matrix became lower. The above changes in SAM group were less obvious when compared with those in I/R group. Conclusion SAM may protect mitochondrion against hepatic ischemia injury, since it may prevent mitochondrial lipid peroxidation, increase ATP, and eventually improve energy metabolism after ischemia-reperfusion.