Gene expression profiles of hippocampi and cerebral cortex of genetical epilepsy-prone P77PMC rats and normal Wistar rats were established by using Atlas^TM Rat cDNA Expression Array. The difference of gene expression profiles was analyzed using image analysis instrument. And 15 differential expression genes were discovered each in hippocampi and cerebral cortex. In the hippocampi, 12 genes were high expression in the P77PMC rats but low expression in the normal Wistar rats, 3 genes were high expression in the Wistar rats but low expression in the P77PMC rats.In the cerebarl cortex,13 genes were high expression in the P77PMC rats but low expression in the normal Wistar rats, 2 genes were high expression in the Wistar rats but low expression in the P77PMC rats. Thus, there are several differential expression genes between P77PMC rat and Wistar rat. All these differentially expressed genes may play important roles in the pathogenesis of epilepsy.