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• The association between ATG5 gene polymorphisms and epilepsy was investigated. • The CC genotype of rs510432 in ATG5 were higher in epilepsy patients. • The CC genotype of rs510432 in ATG5 were higher in late-onset epilepsy patients. • rs548234 were associated with the susceptibility to temporal lobe epilepsy. Autophagy is a highly conserved degradative process that has been associated with a number of neurological diseases. Autophagy-related protein 5 (ATG5) is one of the key genes for the regulation of the autophagy pathway. In this study, we investigated the potential relationship between ATG5 gene polymorphisms and epilepsy in Han Chinese population. We enrolled 112 patients with epilepsy and 100 healthy controls and detected the genotypic and allelic data of 6 single nucleotide polymorphisms (SNPs) in ATG5 (rs2245214, rs510432, rs548234, rs573775, rs6568431 and rs6937876). The associations of 6 SNPs and epilepsy were evaluated. The results revealed the genotypes of overdominant of rs510432 between controls and patients showed significant differences (P overdominant = 0.003). Subgroup analysis showed a highly significant association of rs510432 with late-onset epilepsy (P overdominant = 0.006), and rs548234 were associated with the susceptibility to temporal lobe epilepsy (P codominant = 0.002, P overdominant = 0.006). Furthermore, ATG5 was not linked to either early-onset epilepsy or drug-resistant epilepsy (p > 0.0083). These results demonstrated an association of an ATG5 gene variant with epilepsy, and stronger associations with several subgroups of epilepsy were identified. Our study may provide novel evidence for the role of ATG5 in epilepsy, and contribute to our understanding of the molecular mechanisms of this chronic neurological disease. [ABSTRACT FROM AUTHOR]