The human androgen receptor (AR) gene contains a polymorphic trinucleotide (CAG) repeat sequence in exon 1. The number of CAG repeats may confer differential receptor activity, and specific ranges of variants have been correlated with androgen-sensitive disease processes. Polycystic ovary syndrome (PCOS) is a female condition characterized by androgen excess and infertility, many features of which are effected through the AR. We compared frequency distributions of CAG repeat alleles and their pattern of expression via X-inactivation analysis among 83 fertile women and 122 infertile women with PCOS, all of Australian Caucasian ethnicity. A population comparison with 831 predominantly fertile Australian women was also used. PCR-based assays were used to genotype each woman and assess allele inactivation patterns after digestion of DNA with methylation-sensitive HpaII. Infertile women with PCOS exhibited a greater frequency of CAG alleles or biallelic means greater than 22 repeats compared with both the fertile control group (P < 0.05) and the general population (P < 0.01). Preferential expression of longer CAG repeat alleles was also observed in PCOS and correlated with increased serum T. We conclude that the AR (CAG)n gene locus and/or its differential methylation patterns influence the disease process leading to PCOS.