Human androgen receptor (AR) contains a highly polymorphic polyglutamine tract encoded by CAG repeats [(CAG)n] in exon 1 of the AR gene. The CAG repeats, ranging from 11 to 38, have been reported to be inversely correlated with AR activity. A case-control study involving 261 polycystic ovary syndrome (PCOS) patients and 278 healthy controls was conducted. Fluorescently labeled DNA fragments containing (CAG)n were obtained by PCR and genotyped via capillary electrophoresis. AR (CAG)n ranges were 6, 12-28 in PCOS cases and 9, 10, 12-32 in controls. In the PCOS group, a higher frequency of short (CAG)n alleles was found compared with that of controls (P=0.007). Similarly, CAG biallelic mean distributions also showed statistical difference between the two groups (P=0.025). In conclusion, shorter alleles of the (CAG)n in exon 1 of the AR gene enhanced the susceptibility to PCOS, either by upregulating AR activity or by causing hyperandrogenism.