Autoimmune thyroid disease (AITD) comprises Graves' disease (GD) and Hashimoto's thyroiditis (HT). IL37 has been recently proved to be a natural suppressor for innate immunity and acquired immunity. Therefore, this study was conducted to identify the association of IL37 genetic polymorphisms with AITD in Chinese Han population. Polymorphisms of rs3811046/rs3811047/rs2723176/rs272186 in the IL37 gene were assessed in a case-control study comprising 701 GD patients, 301 HT patients and 939 controls. Genetic variants were genotyped by multiplex polymerase chain reaction and ligase detection reaction. The frequencies of the minor allele A of rs2723176 and A of rs2723186 were significantly lower in the GD patients than in the controls (PZ0.014, ORZ0.774; PZ0.014, ORZ0.777). After gender stratification, the rs3811046 G allele and the rs3811047/rs2723186 A allele were both significantly associated with a decreased risk of GD in female patients (PZ0.030, ORZ0.777; PZ0.023, ORZ0.774; PZ0.029, ORZ0.761). However, none of the four single nucleotide polymorphisms of IL37 gene showed any significant association with HT. Moreover, haplotype analysis revealed the GCG haplotype conferred increased risk for GD as a whole and in female GD patients (ORZ1.213; ORZ1.320). The ACG haplotype was associated with an increased risk of HT as a whole (ORZ1.567) and in male GD patients (ORZ1.820). In contrast, the AAA haplotype showed a protective role for GD as a whole (ORZ0.760) and in female GD patients (ORZ0.765). Our study strongly supports that the IL37 gene variants are associated with the susceptibility to AITD.