Objective To investigate the association between SLC6A11 gene polymorphisms and drug-resistant epilepsy in Chinese Han population.Methods A total of 480 patients with epilepsy who visited the outpatient service of Xiangya Hospital were enrolled according to the inclusion and exclusion criteria. Illumina Golden Gate microarray was used for the identification of SLC6A11 genotypes in 288 patients with drug-sensitive epilepsy and 192 patients with drug-resistant epilepsy. The frequency of monolocus genotypes and the association between haplotype and drug-resistant epilepsy were analyzed.Results The genotype frequencies of 14 single nucleotide polymorphisms (SNPs) of SLC6A11 showed no significant differences between the drug-sensitive epilepsy group and the drug-resistant epilepsy group (P>0.05). The patients with drug-resistant epilepsy had a significantly higher frequency of haplotype 5 than those with drug-sensitive epilepsy (1% vs 4%; OR=2.56; 95% CI 0.107-0.763; P=0.01). However, after the correction of multiple comparisons with Bonferroni's method, we found that the frequency of haplotype 5 showed no significant difference between the two groups.Conclusions Fourteen SNPs of SLC6A11 may not be associated with drug-resistant epilepsy in Chinese Han population.