Abstract: To explore the relationship between the cell-death-inducing DNA-fragmentation factor (DFF45)-1ike effecter-B (CIDE-B) and the neuronal apoptosis after cerebral ischemia reperfusion in rats. The middle cerebral artery occlusion and reperfusion (MCAO/R) models were established by inserting a monofilament suture from left external-internal carotid artery in adult healthy male Wistar rats. The neuronal apoptosis in hippocampus was detected by TUNEL assay, the expression of CIDE-B protein were determined by immunohistochemical staining and Western blot and CIDE-B mRNA by RT-PCR, respectively. After ischemia 2 h and reperfusion 6 h, 1, 3, 7 and 14 days, the No. of neuronal apoptosis was significantly increased (p<0.01) and the expressions of CIDE-B mRNA and protein were evaluated (p<0.01), while all above indexes reduced significantly than those in the control group at reperfusion 28 days (p<0.01). The time-phase of neuronal apoptosis was coincident with the expressions of CIDE-B gene. The neuronal apoptosis was timely dependent on the expression of CIDE-B gene after cerebral ischemia reperfusion in rats.