This study aimed to compare the effects of Metformin and oral contraceptive (cyproterone compound) on serum lipid profiles in patients with Polycystic Ovary Syndrome (PCOS).This randomized controlled trial study was performed on 60 patients with PCOS referred to gynecological clinics of BesatHostpital in Sanandaj , Iran between March 2014 and May 2014.All patients were examined by a researcher, and they were diagnosed with PCOS using the Rotterdam criteria. The participants were randomly allocated into two equal groups (n = 30, each group); one group received Metformin and another group received cyproterone. A written informed consent was obtained from all participants, and then 2 mL blood sample was taken from the participants and sent to the reference laboratory. Data were entered into SPSS version 22 software, and then were analyzed using the Shapiro-Wilk test, mean comparison test, t-test, and Mann-Whitney U test. A statistically significant difference was seen in Triglyceride (TG) levels between the two groups (P < 0.001); so that the level of TG was lower in the Cyproterone compound group compared to the Metformin group, and this difference was increased over time. Also, there was a statistically significant difference in the cholesterol levels between the two groups (P < 0.001). The cholesterol levels were decreased in both groups; however, the level of cholesterol was significantly lower in the Cyproterone compound group compared to the Metformin group, and this difference was increased over time. Moreover, the results showed that there was a statistically significant difference in High-Density Lipoprotein (HDL) and Low-Density Lipoprotein (LDL) levels between the two groups. According to the results of the current study, Metformin treatment has beneficial effects on serum lipid profiles in PCOS.