Background and aims: Berberine (BBR) is an isoquinoline derivative alkaloid isolated from Rhizoma Coptidis traditionally used as anti diarrheic and, more recently, as hypolipidemic and insulin sensitizer agent. Thus, BBR could represent a potential therapeutic option for patients with polycystic ovary syndrome (PCOS). The aim of this study was to evaluate the clinical, metabolic and hormonal effects of BBR in PCOS women. Methods: Fifty oligoamenorrheic PCOS obese women and 50 age and Body Mass Index (BMI) matched healthy controls were enrolled. PCOS women received BBR treatment (500mg, 2 times daily) for 6 months. Clinical and biochemical parameters were assessed before and after the treatment period. Results: Total testosterone (p<0.01), free androgen index (p<0.01), androstenedione (p<0.01), sex hormone binding globulin (p<0.01), progesterone (p<0.01), total cholesterol (p=0.01), low density lipoprotein cholesterol (p<0.01), triglycerides (p<0.01), area under the curve of insulin (p<0.01), menses frequency (p<0.01) and Waist Circumference (p=0.04) significantly (p<0.05) improved after BBR treatment. No correlation was found between variations of insulin sensitivity and hormonal changes. Conclusions: BBR improves clinical, metabolic and reproductive features in PCOS women. Its mechanism of actions need to be elucidated in further studies. © 2013 European Society for Clinical Nutrition and Metabolism.