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Objective: To screen the relative genes associated with the genesis of kindling epilepsy and the effect of caoguo zhimu decoction (CZD) on these genes., Methods: mRNA differential display reverse transcription PCR was used to screen differential gene bind, and Northern blotting hybridization was applied to exclude the false positive reaction., Results: There were as more as 110 differential expression bindings in the normal group, model group and the treated group, among them 11 binds with differential expression only appeared in the model group but not in the normal group and disappeared in the treated group. It indicated that the 11 genes are correlated with the genesis and treatment of kindling epilepsy. By searching in the Gene-bank of NCBI, 7 bindings of the 11 were homologous genes and 4 gene fragments are novel genes with unknown function, which have been registered at the Gene-bank, with the registered numbers of CK325391, CK325392, CK325393, CK325394, respectively, and false positive possibility of 3 novel genes was excluded., Conclusion: CZD has effect in treating kindling epilepsy may be through influencing the expression of partial gene fragments in the hippocampus.