To investigate the distribution of (tttta) n microsatellite polymorphism in the promoter of CYP11a gene in Chinese women with polycystic ovary syndrome (PCOS) and the relationship between such polymorphism and PCOS.Peripheral blood samples were obtained from 201 women with PCOS, aged 26 +/- 4, and 147 women without PCOS, aged 29 +/- 5. Radioimmunoassay was used to examine the levels of testosterone, follicle-stimulating hormone, luteinizing hormone, progesterone, estradiol, and prolactin. Locus-specific prime PCR was used to detect the frequencies of the CYP11a alleles. Body mass index (BMI) was calculated.The average BMI of the women with PCOS was 22 kg/m(2) +/- 4 kg/m(2), and that of the non-PCOS women was 22 kg/m(2) +/- 6 kg/m(2). The six-repeat allele variant genotypic distribution of CYP11a was statistically different between the women with PCOS and those without PCOS [Fisher's exact test (2-tail), P = 0.031]. The frequency of 6//6 genotype in the PCOS patients was 57.7% (116/201), significantly higher than that of the non-PCOS women [44.9% (66/147), chi(2) = 5.588, P = 0.018]. The BMI of the PCOS patients with 4//4 genotype was 19.4 kg/m(2) +/- 1.7 kg/m(2), statistically lower than those of the PCOS patients with 4//6, 6//6, and 6//8 genotypes (23.6 kg/m(2) +/- 3.3 kg/m(2), 22.5 kg/m(2) +/- 3.8 kg/m(2), 22.2 kg/m(2) +/- 4.2 kg/m(2) respectively, P = 0.0037, 0.0027, and 0.059 respectively). The PCOS patients with the allele (tttta) 6 had markedly higher BMI (22.7 kg/m(2) +/- 3.7 kg/m(2)) than those without the allele (tttta) 6 (19.4 kg/m(2) +/- 1.7 kg/m(2), P = 0.0075). No differences were observed in the serum levels of reproductive hormones among the individuals with different genotypic features in the PCOS patients.The six-repeat allele is the most common fragment of (tttta) n microsatellite polymorphism in Chinese Han woman. The 6//6 genotype is significantly more frequent and is associated with greater BMI in the women with PCOS. The six-repeat allele variant may play a certain role in the pathogenesis of PCOS.