Aim: To investigate the possible effects of polymorphisms in genes encoding some important antioxidant enzymes such as super oxide dismutase 2 (SOD2), glutathione peroxidase 1 (GPX1), endothelial NOS (eNOS) and catalase (CAT) in patients with polycystic ovary syndrome (PCOS). Methods: Peripheral blood of 100 patients with PCOS and 100 healthy controlgroup were collected, Polymorphisms in related genes was investigated by using polymerase chain reaction-restriction fragment length polymorphism. In addition, the related biochemical values of the patients were also investigated. Result: In our study there is no significant results for SOD2 gene but the resultsobtained between GPX1, eNOS and CAT genes were significant. Fasting blood sugar (FBS), insulin, triglyceride, waist circumference and... dehydroepiandrosterone sulphate (DHEAS) were found to be significant with the disease, whereas follicle-stimulating hormone (FSH) was found to be effective in preventing the disease. Conclusions: These findings suggest that polymorphisms in genes encoding GPX1, eNOS and CAT enzymes may be associated with PCOS. Additionally, it is thought that the genes of FBS, triglyceride, insulin, DHEAS and waist circumference are important in the pathogenesis of the disease in the presence of homozygous mutation.