Objective This study was performed to examine the invlovement of apoptosis during reperfusion after transient global cerebral ischemia in mice and to investigate the effects of Berberine on it. Methods The model of transient global cerebral ischemia was made by using Pulsinelli-Brierley 4 vessels occlusion methods. Nissl stain was used to observe the morphologic of neuron in the hippocampal CA 1 subfield. Apoptotic cells were detected by TUNEL technique. DNA ladder was observed by agarode gel eletrophresis with hippocampal tissue. Results Berberine reduced evidently the TUNEL positive cells in the hippocampal CA 1 subfield. DNA ladders were detected on agarode gel eletrophoresis at 24 hours and 48 hours during reperfusion after global ischemia,there were no DNA ladders in Berberine group. Conclusion Berberine can reduce apoptosis occuring after global cerebral ischemia in mice.