Evidence indicates that CYP11alpha is a positional and functional candidate for genetic study in polycystic ovarian syndrome (PCOS). In the present study, we have evaluated the association between the CYP11alpha promoter pentannucleotide (tttta)n polymorphism and PCOS among Han Chinese women. Subjects include 125 patients with PCOS and 121 healthy controls, and all were Han Chinese women. Clinical characteristics of patients with PCOS and control subjects were examined according to the Rotterdam consensus criteria. The CYP11alpha promoter pentannucleotide (tttta)n polymorphism was genotyped with PCR and fluorescent capillary electrophoresis protocol. Results indicate that common alleles of the CYP11alpha promoter pentannucleotide (tttta)n polymorphism in this population of Han Chinese women were P4, P6 and P8, and allele P6 was the most common one. Frequencies of those three common alleles between PCOS cases and controls (24.8, 65.6, 6.8% and 23.6, 65.7, 9.9%, respectively) were similar. No significant allelic association of this polymorphism with PCOS was found. However, the carriers with allele P6 among patients with PCOS had increased WHR (0.85+/-0.05 vs 0.82+/-0.08, P=0.039) and decreased AUCG (9.5+/-2.1 vs 11.4+/-2.8, P=0.021) compared to the patients carrying other alleles. Therefore, the most common allele of the CYP11alpha promoter pentannucleotide (tttta)n polymorphism in the population of Han Chinese women is P6, while the most common allele in European Caucasians, as previously reported, is P4. This polymorphism is an ethnic and racial variant, and may have the risk susceptibility in abnormal metabolism of patients with PCOS in Han Chinese women.