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Temporal lobe epilepsy (TLE) is a common and severe epilepsy displaying rhythmicity in humans and animals. However, how the circadian clock contributes to TLE remains elusive. A recent circadian analysis of the ventral hippocampal transcriptome of pilocarpine-induced TLE mice revealed as many as 1650 rhythmically expressed transcripts. Here, a comparison of the mouse ventral hippocampal transcriptome with the human epilepsy-related gene set identified 315 possible mouse epilepsy-related genes. Rhythmicity analysis classified them into arrhythmicity, loss-of-rhythmicity, gain-of-rhythmicity, and rhythmicity-maintaining groups. KEGG and GO analyses of these mouse epilepsy genes suggest their involvement in circadian entrainment. In TLE mice, <i>Htr1d</i>, <i>Drd2</i>, and <i>Chrna3</i> lose rhythmicity, but <i>P2rx7</i> gains rhythmicity; the up-regulation of <i>Htr1d</i> and <i>Drd2</i> and down-regulation of <i>Chrna3</i> inhibit adenylate cyclase (AC), and up-regulation of <i>Htr1d</i>, <i>Drd2</i>, and <i>P2rx7</i> activates protein kinase C (PKC). Together, these results suggest that epilepsy can disrupt the circadian dynamics of the epileptic genes, shed light on possible TLE pathogenesis, and provide potential targets for TLE diagnosis and chronotherapy.