Introduction: Polycystic ovary syndrome (PCOS) is the most common endocrinopathy among women of reproductive age. Women with PCOS commonly display a cluster of metabolic abnormalities, including impaired glucose tolerance, insulin resistance and dyslipidemia. Some recent studies have also shown an association between PCOS and nonalcoholic fatty liver disease (NAFLD). The aim of the present study was to investigate liver enzymes in Iranian women with PCOS and controls to explore determine any possible independent effects of PCOS on liver enzymes. Materials and Methods: Sixty PCOS and sixty non-PCOS women were studied at Vali-e-Asr Hospital of Tehran University. PCOS was diagnosed according to Rotterdam criteria. Data were obtained from patient's files and analyzed using SSPS version 19. Results: Gamma glutam­yltransferase (GGT) level and BMI were significantly higher in PCOS women than in controls (p=0.001). No significant differences were found between groups regarding age or serum levels of Alanine aminotransferase, Aspartate aminot­ransferase, triglycerides, high density lipoprotein, low density lipoprotein, fasting glucose, fasting insulin levels and HOMA-IR. GGT was significantly higher in lean PCOS women compared to their controls (p=0.002), although there was no significant differences in GGT levels between overweight/obese PCOS women and overw­eight/obese controls, and hence no correlation between BMI and GGT. Conclusion: Considering the association between PCOS and NAFLD, women with PCOS should be screened for liver disease.