Background: Genetic factors are significantly have important role in the etiology of the polycystic ovary syndrome (PCOS). This study examined the possible relation of rs1484215 and rs6495096 polymorphisms of CYP11A1 gene in Iranian women with PCOS. Methods: The population of the case-control research included 100 women presenting with PCOS and 100 women as a control group who were referred to Infertility Center in Qom, Iran. The genotypes of rs1484215 and rs6495096 polymorphisms in CYP11A1 gene were detected with the tetra-ARMS PCR method. The independent segregation of alleles was tested for the Hardy–Weinberg equilibrium (HWE). Differences in quantitative traits were assessed between each group with a single PCOS feature and control group using Mann–Whitney U test for categorical variables and student’s t-test for continuous variables. Statistical analysis of allele and genotype frequencies between women with PCOS and control was performed using the chi-square test. Significance level was defined as p<0.05. Results: There was a significant association of C with G alleles in rs6495096 polymorphism and susceptibility to PCOS (p=0.001), but no significant relation was found between C and T alleles in rs1484215 polymorphism and susceptibility to PCOS. Also, GG genotype of rs6495096 was significantly associated with the waist-to-hip ratio (WHR) and infertility duration compared to CG and CC (p0.01). However, rs1484215 showed no association with these variables. Conclusion: The results from the research indicated that rs6495096 polymorphism of CYP11A1 gene is related to the PCOS risk in Iranians women.