Polycystic ovary syndrome is a common pathology in women of reproductive age, leading to hyperandrogenism, dyslipidemia, diabetes mellitus, ovulation disorder and infertility. Etiopathogenesis of the disease is actively studied, but many of its mechanisms are unclear. The aim was to study the frequency of IL6 and vitamin D receptor gene polymorphisms, blood contents of vitamin D in polycystic ovary syndrome combined with autoimmune thyroiditis.A total of 192 women were examined, the average age of the patients was 25.5±3.1 years; of these, 130 women had polycystic ovary syndrome. The patients were divided into 2 groups: with polycystic ovary syndrome combined with autoimmune thyroiditis (1st group) and olycystic ovary syndrome without autoimmune thyroid pathology (2nd group); 62 healthy women made up the control sample. The ELISA method was used to determine thyroid stimulating hormone, thyroid hormones, antibodies to thyroid peroxidase, vitamin D, testosterone, estradiol, progesterone, 17-hydroxyprogesterone, luteotropic hormone, follicle-stimulating hormone. Material for genetic studies was isolated from buccal cells. The typing was performed by PCR, and the following polymorphisms were tested: IL6 (rs1800795 SNP), vitamin D receptor (VDR) gene (rs1544410), DHCR7 (rs12785878), GC (rs2282679), CYP2R1 (rs10741657). The results were as follows: polymorphism of IL6, VDR, DHCR7, GC, CYP2R1 genes was revealed in the patients with polycystic ovary syndrome in combination and without concomitant autoimmune thyroiditis. The lowest levels of 25-hydroxyvitamin D in serum were found in the patients with polycystic ovary syndrome and autoimmune thyroiditis.Polymorphism of IL6 genes, vitamin D receptor, DHCR7, GC, CYP2R1 genes may aggravate the course of polycystic ovary syndrome and requires a more comprehensive study. When polycystic ovary syndrome was combined with autoimmune thyroiditis, the studied gene polymorphisms did not differ significantly from those in patients with polycystic ovary syndrome without autoimmune thyroiditis, thus suggesting greater significance of these genetic factors in pathogenesis of polycystic ovary syndrome. However, more than a half of women with combined endocrine disorders had both homozygous and heterozygous variants of pathological IL6 gene carriage along with lowest vitamin D levels, which may significantly affect immune response and, hence, determine the development of both endocrine disorders.