Objective：To investigate the activation law of autophagy related protein-12（Atg12） and autophagy microtubule-associated protein light chain 3 antibodyⅡ（LC3-Ⅱ） in the cerebral cortex during focal cerebral ischemia-reperfusion injury（CIR），and to fur－ther explore its influence on brain autophagy on this basis. Methods：The rats were divided into sham operation group（sham group） and ischemia reperfusion group（CIR group），and the CIR group was subdivided into six subgroups：CIR 0，6，12，24，48h and 72 h. Ex－cept that sham group and CIR 24h group had 20 rats in each group（10 were used for model identification），there were 10 rats in other groups，respectively. Focal CIR model was established by middle cerebral artery occlusion. CIR model was identified by neurological score，2，3，5-Triphenyltetrazolium chloride（TTC） staining，and brain water content 24 h later. The expression pattern of Atg12 and LC3-Ⅱ in cerebral cortex was detected by immunohistochemistry methods and Western blot techniques. Results：Compared with sham group，there were obvious neuro－logical deficit symptoms，cerebral infarction and cerebral edema in CIR 24h group. The results of immunohistochemistry showed that the positive rates of Atg12 and LC3-Ⅱ appeared in rat CIR 6 h[（15.49±4.18）%，（18.54±3.62）%]，and peaked at 24 to 48 h[（33.63±3.26）%，（29.62±1.73）%]，then the expression gradually decreased 72 h later[（24.90±3.96）%，（20.36±3.51）%]. The results of Western blot showed that the expression of Atg12 and LC3-Ⅱ appeared in rat CIR 6 h[（0.372 3±0.076 5），（0.148 4±0.011 5）]，and peaked at 24 to 48 h [（0.741 7±0.071 8），（0.451 3±0.019 0）]，then the expression gradually decreased 72 h later[（0.365 0±0.042 0），（0.245 1±0.030 3）]. Conclusion：The expression of Atg12 and LC3-Ⅱ plays an important role in the regulation of brain autophagy during the CIR.