One characteristic of polycystic ovary syndrome (PCOS) is hyperandrogenism, which may be related to the activity of androgen receptor (AR). This study was designed to investigate the polymorphism of CAG and GGN repeats in the AR gene in women with PCOS. The frequency distributions of CAG and GGN repeat alleles, as well as their X-inactivation patterns, were compared between 76 age-matched normal women (control group) and 80 women with PCOS (PCOS group). The expression of AR mRNA in the ovarian tissues of seven patients with PCOS and five normal women was also tested using real-time quantitative PCR.