AIM: To explore the relationship between the expression of caspase-2 and caspase-3 and the apoptosis in retinal ischemia/reperfusion (I/R) injury of rats, as well as the therapeutic effects of brain derived neurotrophic factor （BDNF）on the ischemic and reperfused retina. · METHODS: This experiment was conducted at the laboratory of Affiliated Hospital of Qingdao University Medical College from February 2007 to July 2007. The models of retinal ischemia/reperfusion injury were made by transiently elevating intraocular pressure. A total of 28 rats were divided into normal and operative groups. Operative group was divided into six subgroups. In each subgroup there were four rats. The left eyes of rats were used for I/R and the right eyes were used for intravitreal injection of brain-derived neurotrophic factor (BDNF) as treatment group. After reperfusion we divided our subgroups according to the reperfusion time as 1, 6, 12, 24, 48, 72 hours. The retinal ganglion cell number was counted by using optic microscope (BX-51,Olympus). Apoptosis was assessed by the terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labelling (TUNEL) method, and the expression of caspase-2, caspase-3 was studied by enzyme linked immunosorbent assay (ELISA) and strept avidin-biotin complex (SABC) immunohistochemistry. ·RESULTS: No positive apoptotic cells were observed in the normal rats' retinae, but there were a significant number of positive apoptosis cells in 6-24 hours after transient ischemia followed by a decrease at 48 hours. The number of apoptotic cells reached a maximum at 24 hours after ischemia .The expression of caspase-2 gradually increased as early as at 6 hours, reached a peak at 24 hours, then decreased between 48 and 72 hours. Similarly, caspase-3 has the same rule with caspsae-2 in the time courses of expression in retinal tissues. BDNF administered before reperfusion inhibited the expression of apoptosis and ameliorated the retinal tissue damage. It also decreased caspase-2 and caspase-3 expression in ischemic/reperfused retina. ·CONCLUSION: Retinal ischemia-reperfusion can induce apoptosis of cells in the retina. BDNF rescues retinal ganglion cells (RGCs) fromretinal ischemia/reperfusion injury through down-regulation of cell apoptosis and caspase-2 and caspase-3 expression. BDNF have a neuroprotective effect on retina.