AbstractObjective. We examined the influence of the androgen receptor gene (AR) CAG microsatellite (AR‐CAG) repeat polymorphism and X‐chromosome inactivation (XCI) pattern on ovarian reserve markers (follicle stimulating hormone (FSH) and antral follicle count on menstrual cycle day 3–5) and disease etiology in patients with polycystic ovarian syndrome (PCOS) or premature ovarian failure (POF). Design. Case‐control study. Population. In all, 32 women with PCOS, 26 women with POF and 79 controls were investigated. Methods. AR‐CAG and XCI were analyzed using polymerase chain reaction‐based assays following DNA digestion with the methylation‐sensitive restrictase HpaII. Main outcome measures. Distribution of AR‐CAG alleles and XCI patterns. Results. POF patients had shorter AR‐CAG microsatellites than controls. AR‐CAG microsatellite length was negatively associated with serum dehydroepiandrosterone sulfate level. The magnitude of XCI skewing was negatively and positively correlated with luteinizing hormone (LH) and FSH serum levels, respectively, during the early follicular phase, but showed no correlation with the number of early antral follicles. Conclusions. Our results suggest that AR‐CAG variations and XCI pattern exert an effect on FSH and LH values, and also have the potential to influence the etiopathogenesis of POF.