Objectives: To evaluate the role of anti-Mullerian hormone (AMH) and inhibin B in the evaluation of the effectiveness of short- (3 months) and long-term (6 months or more) metformin therapy in Iraqi women with polycystic ovarian syndrome (PCOS). Methods: This cross-sectional study was carried out at the Biochemistry Department, College of Medicine, University of Baghdad, Baghdad, Iraq from June 2010 to May 2011. It included 38 volunteers of women patients with PCOS, aged 18-38 years, who were classified into: Group I (GI, n=20); Group II included women in GI that were followed up after they were treated with metformin hydrochloride tablet 500 mg 3 times daily for 3 months; and GIII included 18 women that were already on metformin hydrochloride treatment 500 mg tablet 3 times daily for 6 months to 3 years. Investigations included serum measurement of insulin, AMH, inhibin B, androgen hormones using enzyme-linked immunosorbent assay, and mini Vidus techniques. Results: The mean ± standard error of the mean value of serum AMH levels was significantly decreased in post metformin treatment women (3 months; GII) compared with those before treatment (GI), and those women on prolonged treatment (GIII) ( p