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To study the effect of late reperfusion on caspase-3 activity of ischemic myocardium in rabbit and its significance. Methods 24 adult rabbits were randomly divided into3 groups: Sham ( S ) without ligation of coronary artery, Late Reperfusion (LR) with ligation for 3 hours following release for 3 hours and Persistent Ischemia (PI) with persistent ligation of coronary artery for 6 hours. All animals were sacrificed 6 hours after the beginning of the experiments. Border region of infarcted myocardium were incised for analyzing the concentration of SOD, MDA, GR and the expression of FADD, Caspase-3 and the apoptosis index (AI). Results Compared with the Sham group, LR and PI group exhibited much higher MDA, FADD, Caspase-3, AI and much lower SOD, GR(all P <0.01 ). Compared with the PI group, LR group exhibited higher MDA, FADD, Caspase-3, AI and lower SOD, GR ( all P<0.05 ). Conclusions Late reperfusion markedly enhanced the Caspase-3 activity and then the number of apoptotic cardiomyocyte in border region of infracted myocardium, which indicated the existence of late reperfusion injury. The mechanism may involve the high oxidative stress state and expression of FADD.