Objective To investigate the effects of chloroquine on the expressions of autophagy related proteins after focal cerebral ischemia-reperfusion in adult rats. Methods A total of 75 healthy SD rats were randomly allocated to sham-operation, model and chloroquine(CQ) 20,40 and 60 mg/kg groups. A model of middle cerebral artery occlusion (MCAO) for 2 h was induced by suture method. The CQ 20,40 and 60 mg/kg groups were injected intraperitoneally immediately following MCAO in the 3 medication groups. Neurological deficit scores and TTC staining were evaluated, and then the expressions of autophagy related proteins in area of cerebral ischemia-reperfusion were analyzed by immunofluorescence and Western blot technique at 24 h after reperfusion. Results ①Neurological deficit scores in the sham-operation, model, CQ 20, 40 and 60 mg/kg groups were 0, 2.67±0.49, 2.93±0.26, 2.40±0.51 and 1.93±0.7 respectively. Compared with the infarction area of the model group by TTC staining, the CQ 20 mg/kg group was significantly increased, the CQ 40 mg/kg group was almost like the model group,the CQ 60 mg/kg group was significantly decreased. ② Compared with the model group, the results of immunofluorescence and Western blot technique showed only a trace expressions of proteins(Atg5, Atg7, Beclin1 and Atg12 ) in the sham operation group (P<0.05), and the same pattern of expressions were observed in the CQ 20 mg/kg group. However there was significantly reduced expressions in the CQ 60 mg/kg group (P<0.05). Conclusion The CQ have has two fold effects, i.e., the CQ 20 mg/kg group can aggravate the damage, whereas the CQ 60 mg/kg can alleviatereduce the damage. The mechanism of CQ in the prevention and treatment of cerebral ischemia-reperfusion injury in rats may be associated with the dose of the expressions of some autophagy related proteins.