Objective: To study the polymorphism TaqIB (rs708272) gene protein cholesterolоl ester transfer (CETP) in women with autoimmune thyroiditis. Materials and Methods: We examined 98 women with autoimmune thyroiditis, mean age 55.2 ± 7.8 years, disease duration 8.0 ± 6.4 years, menopause duration 6.4 ± 3.5 years. The average dose of L-thyroxine 84.3 ± 28.5. Control group consisted of 135 women of similar age without thyroid pathology. Polymorphism of TaqIB (rs708272) CETP gene formed by PCR RFLP on published by technique. Results: As a result, it was found that in the group of women with AIT В1В1 and В2В2 genotypes determined in 37.8 % and 21.4 %. Win В1В2 heterozygotes in patients with hypothyroidism compared with the control group was significantly lower: 40.8 % and 54.8 %, p = 0.035. Average levels of total cholesterol, LDL cholesterol, HDL cholesterol, triglycerides were not significantly different in carriers of different genotypes of TaqIB polymorphism (rs708272) CETP gene in the two groups.