Aim: To investigate differential gene expression and the pharmacological mechanism of baicalin and gardenin in focal cerebral ischemia in rats with high-density cDNA microarray. Methods: Rat left middle cerebral arteries were occluded and treated with either baicalin or gardenin. The pharmacological effects were investigated using the difference in infarction areas before and after treatment, which were determined by 2,3,5-triphenyltetrazolium chloride (TTC) staining. Gene expression was demonstrated using a "Biostar40S" gene microarray. Semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) was used to verify the result of the selected genes. Results: Both baicalin and gardenin reduced the infarction areas in focal cerebral ischemia rats (P＜0.05). The differential genes were 211,177, and 70 (upregulated or downregulated) in the model group, baicalin,and gardenin treatment groups compared with the sham-operated group,respectively. Gene expression of RpL19 and Csnk2 underwent an approximately 1.9 and 2.1-fold increase, respectively, verified by semiquantitative RT-PCR, which was the same trend as the cDNA microarray. Conclusion: Differential gene expression with respect to the pharmacological effects of baicalin and gardenin on focal cerebral ischemia by cDNA microarray revealed a number of clues with respect to the therapeutic mechanisms of Chinese traditional medicine. In addition,the present study provided theoretical and experimental evidence that will aid future studies examining cerebral ischemia.