Objective To investigate the effects of brain-derived neurotrophic factor (BDNF) pretreatment on neuron apoptosis and the expression of Bcl-2 and Bax protein following global cerebral ischemia-reperfusion (I/R) injury in gerbils. Method Forty-eight mongolian gerbils were randomly divided into six groups in equal number (n = 8): normal control group (group C), ischemia-reperfusion group (group I/R) and four BDNF pretreatment groups according to various lengths of time from BDNF pretreatment to ischemia-reperfusion. The BDNF pretreat-ment was carried out in gerbils with lateral ventricular injection of BDNF 0.5μg 6 h, 12 h,24 h and 48 hours be-fore cerebral ischemia, and those gerbils assigned into PR6, PR12, PR24 and PR48 groups. The global cerebral is-chemia-reperfusion was induced by occlusion of bilateral common carotid arteries for 20 minutes and then the arter-ies were released for 24 hours reperfusion. The confirmation of global cerebra ischemia was evidenced by the ap-pearance of mydriasis and disappearance of light reflex and righting reflex. Twenty-four hours later, all gerbils including those of control group were sacrificed and a piece of tissue was taken from frontal cortex just behind the optic chiasma 1～4 millimeter for making paraffin sections. Neuron apoptosis was identified by using TUNEL and immunohischemistry was used to detect the expression of Bcl-2 and Bax protein in cerebral cortex. The data were analyzed by using analysis of variance. Results There were no apoptotic cells, and expression of Bcl-2 and Bax protein positive cells found in group C. Neuron apoptosis in brain cortex was detected in I/R group and BDNF pre-treatment groups. The indexes of neuron apoptosis in BDNF pretreatment groups were markedly lower than those in group I/R (P < 0.01). Compared with group I/R, the index of expression of Bcl-2 protein positive cells was in-creased significantly in BDNF pretreatment groups (P = 0.005), while the index of expression of Bax protein posi-tive cells were decreased significantly (P < 0.01 in all groups). Among 4 BDNF pretreatment group, the lowest apoptosis index and lowest of expression of Bax protein positive cells were found in PR6 and PR12 BDNF pretreat-ment groups (P = 0.0056 and 0.001, respectively). Conclusions Different time windows of BDNF pretreatment can decrease the neuron apoptosis in different degree, and protect brain against cerebral ischemia-reperfusion injury significantly. Among BDNF pretreatment time windows, pretreatment of 6 hours and 12 hours are the better ones.The mechanism of protection of BDNF pretreatment may be attributed to inducing Bcl-2 protein expressions and in-hibiting Bax protein expressions, and thereby inhibiting neuron apoptosis.