To investigate the association between polymorphism of cytochrome P450 subfamily XIA polypeptide 1 (CYP11A1) gene and polycystic ovarian syndrome (PCOS) in Chinese population.From May 2005 to Dec. 2008, 290 PCOS cases treated in the First affiliated hospital of Anhui Medical University matched with 344 reproductive women as controls were enrolled in this study. Genotypes of 7 tagging single nucleotide polymorphisms (tSNP, rs12438594, rs4077582, rs9806234, rs16968477, rs4887139, rs1843090, rs11632698) covering CYP11A1 gene (r(2) > or = 0.8) and 3 microsatellite markers (D15S1547, D16S520, D15S1546) were chosed from the phase II database of Han population in HapMap data. Genotype and frequency of allele were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and haplotype of gene polymorphism were analyzed in 290 PCOS cases and 344 controls.Among 7 tSNPs and 3 microsatellite markers, the frequency of rs4077582, D15S1547, D15S1546 and rs11632698 between two groups reached statistical difference (P = 0.010, 0.044, 0.018 and 0.026). The allele frequency of rs4077582, rs4887139, rs1843090, D15S1547 and D16S520 showed significant difference between two groups (P = 0.002, 0.048, 0.030, 0.001 and 0.024). Among 5 haplotype of CYP11A1 (ACGCA13/6/9AG, ACGTA16/6/11AA, GCACG12/8/8AA, GTACA14/4/7GG, GTGCA13/6/7AG), the frequency of GTACA14/4/7GG and ACGCA13/6/9AG were 7.8% (45/580) and 25.3% (147/580) in PCOS group and 11.9% and 19.6% in control group, which showed statistical difference (P 0.05).The polymorphism of CYP11A1 gene was associated with PCOS, however, the relationship between gene sequence covered by tSNP/microsatellite markers and hyperandrogenism of PCOS should be further investigated.