Although the connection between SEPS1 gene variants and Hashimoto's thyroiditis (HT) has been established in Europeans, the relationship between the SEPS1 gene and HT remains unclear in Han Chinese. Here we aimed to investigate the potential association between SEPS1 variants and HT in the Han population. In addition, the effects of SEPS1 haplotypes on the susceptibility of the development of immune-mediated diseases with an inflammatory component will also be evaluated. Seven single-nucleotide polymorphisms (SNPs) with minor allele frequency ⩾0.05 were genotyped in 1013 HT patients and 2998 healthy controls from genetically independent Han Chinese individuals. We identified that the rs28665122 SNP was significantly associated with HT, both in the female group (allelic P=0.002644 and genotypic P=0.010326) and the combined data set (allelic P=0.000518 and genotypic P=0.002731). Further analyses based on haplotypes indicated that a two-SNP haplotype (rs2009895-rs28665122) was significantly associated with HT (global P=0.0036), which was also observed in females (global P=0.0162) but not in males. Our findings provide further supporting evidence that confirms the results of previous studies, which suggested potential roles of the SEPS1 gene in the pathogenesis and etiology of HT.