Research questionAre the combined genotypes and haplotypes of VDR gene polymorphisms (FokI, ApaI, TaqI) associated with PCOS susceptibility and metabolic features of the disease? DesignWe performed a case-control study, including 46 women with PCOS and 48 controls. Genotypes of VDR genes were determined using the PCR-RFLP (restriction fragment length polymorphism) method. In all women, the waist circumference, parameters of lipid and glucose metabolism were evaluated. ResultsPCOS group presented higher waist circumference and visceral adiposity index (VAI) levels compared to controls. Total cholesterol, LDL-C and triglycerides had higher values in PCOS women. VDR-FokI C/C (F/F) genotype had significantly higher odds of PCOS (adjusted OR = 6.27, 95% CI: 1.53-25.65). VDR-Apal was associated with susceptibility to PCOS in the dominant model, the variant genotype (A/C-A/A) (A/a- a/a) had higher odds of PCOS than the wild genotype C/C (A/A) (adjusted OR = 3.15, 95% CI: 1.07-9.32). Haplotype analysis revealed that T-C- T (f-A-T) haplotype was statistically associated with lower odds of PCOS (adjusted OR = 0.10, 95% CI: 0.01-0.95). PCOS women with VDR-Fokl T/T (f/f) genotype had lower fasting glucose and higher VAI levels compared to C/T (Ff) or C/C (F/F) genotype. ConclusionThe present findings suggest the association between FokI and ApaI polymorphisms and PCOS susceptibility. Moreover, T/T (f/f) genotype of VDR-FokI could be a marker of decreased fasting glucose in PCOS. TaqI polymorphism did not reveal a relationship with PCOS susceptibility in our study population.