Objective To investigate the effects of inosine on the neuronal apoptosis and the expression of cytochrome C mRNA after focal cerebral ischemia and reperfusion in rats,and to explore the neuroprotective mechanisms of inosine. Methods SD rats model of focal ischemic reperfusion was induced by intraluminal middle cerebral artery occlusion (MCAO) with a nylon monofilament suture. Inosine (100 mg/kg) was injected intraperitoneally twice following MCAO. Apoptosis was determined by terminal deoxynucleotidy1 transferase-mediated uridine 5'-triphosphate-biotin nick end -labeling (TUNEL) staining. In situ hybridization was performed to examine the expression of cytochrome C mRNA. Results TUNEL-positive cells were observed 2 h after reperfusion and peaked at 1 d and 2 d after reperfusion in cortex and striatum respectively. Inosine reduced the number of TUNEL-positive cells at and after reperfusion 12 h. Cytochrome C mRNA expressed in cortex and striatum of ischemic hemisphere as early as at 2 h after reperfusion and reached a peak at 12 h and 1 d in cortex and striatum respectively. Inosine could diminish the expression of cytochrome C mRNA at and after reperfusion 12 h. Conclusions Inosine might play a neuroprotective role by inhibiting the neuronal apoptosis and the expression of cytochrome C mRNA which were induced by cerebral ischemia reperfusion injury.