The aim of the present study was to investigate the effect of polydatin on apoptosis induced by ischemia/reperfusion (I/R) in rat myocardium and to explore the underlying mechanism. Adult male Sprague-Dawley (SD) rats were randomly divided into control, I/R and polydatin (50 mumol/L) groups. On the Langendorff apparatus, isolated rat heart was subjected to 30-min global ischemia followed by 60-min reperfusion. TUNEL labeling and flow cytometric techniques were used for the measurement of apoptosis and the expression of Bcl-2 and Bax protein in cardiomyocytes of rat. The results showed: (1) Compared with those in the control group, the number of TUNEL-positive cells and apoptosis rate were increased in I/R group; (2) Compared with that in the I/R group, the number of TUNEL-positive cells was significantly decreased in the polydatin group [(18.1+/-4.0)% vs (35.1+/-5.4)%, P<0.01]; (3) Apoptosis rate assayed by flow cytometry in I/R group was significantly higher than that in polydatin group [(15.43+/-4.55)% vs (8.66+/-3.18)%, P<0.01]; (4) Expression level of Bax protein was higher in I/R group than that in polydatin group (P<0.05), while the level of Bcl-2 protein and Bcl-2/Bax ratio were higher in polydatin group than those in I/R group (P<0.05, P<0.01), respectively. The results obtained suggest that polydatin exerts an inhibitory effect on I/R-induced apoptosis through increasing Bcl-2 protein expression and decreasing Bax protein expression in myocardium of the rat.