Aim To investigate the effect of gemfibrozil on myocardium ischemia/reperfusion injury in hypercholesterolemic rabbits. Methods Twenty-four New Zealand white rabbits were divided into ischemia reperfusion (I/R) group, gemfibrozil treatment and ischemia reperfusion group, and sham operation group, which were fed with high cholesterol diet for 9 weeks to establish hypercholesterolmia rabbits model. And 200 mg/(kg·d) gemfibrozil was given for a week in gemfibrozil group on the nineth week. Acute myocardial ischemia reperfusion injury model was built through ligating the left anterior descending of coronary artery in rabbits. The serum lipid levels were measured in the different experiment stages. The ultrastructure of the myocardial cells by transmission electron microscope was observed and the sizes of infarct myocardium were detected in each group. The expression of peroxisome proliferator-activated receptor alpha (PPARα) and fatty acid translocase (CD36) mRNA were detected by reverse transcription polymerase chain reaction(RT-PCR). Results Rabbits fed with cholesterol-riched diet showed higher serum levels of total cholesterol(TC), low density lipoprotein cholesterol (LDLC) (P<0.05). Gemfibrozil did not change serum lipids levels during the feeding period. The ultrastructure of myocardium cell was slightly destroyed and the myocardial infarct size was significantly smaller in gemfibrozil treatment group than I/R group. The mRNA levels of PPARα and CD36 were decreased in I/R group compared with sham operation group, and there were no difference between gemfibrozil treatment group and sham operation group. Conclusion The short-term gemfibrozil treatment reduced the myocardial infarct size and up-regulted expression of PPARα and CD36 mRNA in myocardial after ischemia/reperfusion.