Objective To investigate the effects of hypoxic preconditioning (HPC) and middle cerebral artery occlusion (MCAO) on microRNAs expression in the brain of mice.Methods miRNA microarray was used to detect the changes of miRNA expression in the cerebral cortex of HPC mice and the peri-infarct region of MCAO mice.Results Among 656 probes，the expression of 17 miRNAs changed significantly in the cerebral cortex of HPC mice compared with those of control group (P<0.05，n=12).Sixty-five miRNAs changed dramatically in the peri-infarct region of MCAO mice (n=12) compared with those of the sham control group (P<0.05，n=12).The expression pattern of 33 miRNAs changed in the peri-infarct region of the HPC and MCAO group (n=12) compared with the peri-infarct region of the MCAO mice (P<0.05，n=12).Based on Diff Score= ±13 (P= 0.05)，19 differentially expressed miRNAs both changed in HPC and MCAO mice.Then，four miRNAs from the 19 specified miRNAs were randomly chosen as the candidates for verification in HPC and MCAO mice by using qRT-PCR.Conclusions The expression of 19 miRNAs significantly changed in the brain of HPC and MCAO induced-focal cerebral ischemia mice which might involve in cerebral ischemic/hypoxic injuries and HPC-induced neuroprotection.