The autoimmune thyroid disorders, or AITDs, comprise 2 related disorders, Graves' disease and Hashimoto thyroiditis. In AITD, immune system produces antibodies against autothyroid antigens. The etiology of AITDs involves a complex interaction between genetic predisposing factors and environmental triggering factors. Variations in NACHT leucine-rich repeat protein 1(NLRP1) gene a key regulator of the innate immunity have been shown to confer risk for vitiligo and several autoimmune diseases. In this study we hypothesize that variants in NLRP1 gene might be involved in the susceptibility to autoimmune thyroid disease. Five single nucleotide polymorphisms (SNPs) in NLRP1 were genotyped in 207 AITD patients and 220 normal controls. We found that NLRP1 rs12150220 T allele (OR = 1.273, 95% CI: 0.971-1.670, p = 0.040) and NLRP1 rs2670660 G allele (OR = 1.264, 95% CI: 0.965-1.656, p = 0.044) were significantly associated with AITD compared with controls. These results suggest that NLRP1 may be involved in the pathogenesis of AITD.