Polycystic ovary syndrome (PCOS) is a common health problem that affects women in childbearing age. Recent studies discussed the relation of oxidative stress with PCOS and suggested that the antioxidants may improve the prognosis of PCOS. Changes happened in ATP binding cassette transporter 1 (ABCA1) gene encoding a protein regulating entry and exit from cell membrane may contribute to dyslipidemia in patients with PCOS. The role of oxidative stress and ABCA1 gene polymorphism in the pathogenesis of PCOS was evaluated along with the effect of antioxidants in the prevention and treatment of this disease. The present study included 90 female patients with PCOS and 90 healthy women represented the control group. Patients with PCOS were further divided into two subgroups. The patients included in subgroup 1a were treated with antioxidant and hormonal therapy while patients included in subgroup 1b were treated with hormonal therapy only. ABCA1gene polymorphism and oxidative stress parameters were investigated in all groups. The level of the oxidant marker; MDA was higher in PCOS patients when compared to controls. In addition, the levels of GSH, vitamin E, ascorbic acid, and selenium were significantly decreased, while SOD and GPx activities were increased in PCOS patients when compared to controls. The response to treatment among PCOS patients was better in group 1a than group 1b. The frequency of ABCA1 AA genotype was higher in PCOS patients than the control group (32.2% and 11.1% respectively). It was concluded that oxidative stress may lead to PCOS which raises the possibility of using antioxidants for the prevention and control of PCOS. In addition, the polymorphism in ABCA1 gene may be associated with genetic susceptibility for PCOS.