To investigate the molecular mechanisms of neuronal loss and mossy fiber sprouting in hippocampus of pilocarpine-induced epileptic rats. The epileptic rats induced by pilocarpine and the hippocampi were removed at 7 days after status epilepticus. The protocol of the differential display polymerase chain reaction (DD-PCR) was adapted to screen for differentially-expressed fragments of genes at the transcription level in the rat hippocampus. It was shown that there were 13 genes differentially expressed in the seventh day of epileptic rats. There were 7 genes were up-regulated in the epileptic rat including ATPase synthase subunit 6, GATA binding protein 3, Dstonin, Glutamate receptor I, Psmd11_predicted, Timm23 and App; and 6 genes were down-regulated in the epileptic rat including NG5 protein, Calmodulin1, NGF-IA, Fbxo38_predicted, PAF-AH beta and EPR13.