The Autoimmune thyroid diseases (AITDs) are among the most common endocrine disorders. Vitamin D as an immunomodulator and Vitamin D receptor (VDR) gene polymorphisms may be effective in AITDs pathogenesis. The aim of this study was to evaluate the vitamin D level and VDR BsmI and TaqI polymorphisms in Iranian Azeri Turkish patients with AITDs. This case-control study included 121 adults with AITDs and 117 non-AITDs controls. Serum level of 25-hydroxyvitamin D was measured by electrochemiluminescence (ECL) immunoassay. BsmI and TaqI polymorphisms were assessed by polymerase chain reaction fragment length polymorphism technique. The serum level of 25-hydroxyvitamin D in AITDs patients were lower than controls (P=0. 03). The frequencies of TT, TC, CC, T and C genotypes/alleles at TaqI (rs731236) marker were 52. 1%, 34. 7%, 13. 2%, 69. 4% and 30. 6% in AITDs and 44. 4%, 41. 9%, 13. 7%, 65. 4% and 34. 6% in controls, respectively. The frequencies of AA, AG, GG, A and G genotypes/alleles at BsmI (rs1544410) marker were 14%, 64. 5%, 21. 5%, 46. 3% and 53. 7% in AITDs and 26. 5%, 58. 1%, 15. 4%, 55. 6% and 44. 4% in controls, respectively. BsmI (rs1544410) GG+AG genotypes and G allele were more frequent among patients with Hashimoto compared with control group (86. 6% vs. 73. 5% (OR: 2. 34, 95% CI: 1. 16-4. 70, P = 0. 014) and 54. 29% vs. 44. 44% (OR: 1. 48, 95% CI: 1. 02-2. 15, P = 0. 038), respectively). Vitamin D status can be related to AITDs pathogenesis. BsmI (rs1544410) GG+AG genotypes and G allele may play an important role in the predisposition to Hashimoto.