AIM This study was done to illustrate the clinical and biochemical effects of ethinyl estradiol-cyproterone acetate (EE-AC) and metformin in this disease. METHODS This was a randomized control trial study, done on twenty-six female patients already diagnosed as cases of PCOS. Participants were divided into two study groups: group one (Group 1), received metformin of 500mg twice daily and the second group (Group 2), was given ethinyl estradiol-cyproterone acetate for 21 consecutive days followed by 7 days drug-free. The course of the treatment for both groups was continued for three consecutive months. RESULTS Group 1 showed a statistical significant increase in serum high density lipoprotein cholesterol (HDL-C) levels (P=0.006) and a decrease in the level of triglyceride (TG) (P=0.006). In addition, Group 1 had a significant reduction in the levels of very density lipoprotein cholesterol (VLDL-C) (P=0.006). Group 2 had a significant increase in serum TG levels (P=0.01), associated with a significant decrease in serum LDL-C (P=0.04). Serum testosterone was significantly reduced in group 1 (P=0.038). This was associated with an improvement in glucose tolerance test (GTT) and BMI in the same group (group 1). Group 2, had an improvement in the menstrual cycle control; hirsutism and acne. CONCLUSION This study showed that metformin treatment is beneficial in improving serum lipids; glucose homeostasis and BMI, however, the ethinyl estradiol-cyproterone acetate is superior in improving the clinical manifestation of patients with PCOS, including menstrual cycle regulation, hyperandrogenic state.