Objective To investigate the effects of pioglitazone on serum leptin and adiponectin in polycystic ovary syndrome (PCOS) patients with insulin resistance (IR). Methods Thirty-five PCOS patients with IR were treated with pioglitazone 15mg/d for 12 weeks. The results of ovulation induction were observed. The changes of fasting plasma glucose (FPG), fasting serum insulin (FINS), serum levels of leptin, adiponectin, follicle-stimulating hormone (FSH), luteinizing hormone (LH), testosterone (T) and blood fat were examined at the baseline and after the therapy by enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay (RIA). Results After the treatment, the rate of ovulation per cycle was improved in 31 (88.5%) out of the 35 patients. After treatment, the level of serum leptin was decreased (P<0.05) while the level of serum adiponectin was increased (P<0.05). After 12 weeks'treatment, waist-to-hip ratio and F-G score were significantly decreased (P<0.05), BMI declined but without significant difference (P>0.05). The levels of LH, T, FINS, Homa-IR, total cholesterol, triglyceride and low density lipoprotein-cholesterol were significantly decreased (P<0.01, P<0.05), whereas the level of high density lipoprotein-cholesterol was significantly increased (P<0.01). No significant difference was seen in FSH and FPG following treatment (P>0.05). Conclusion Pioglitazone treatment can effectively improve PCOS with IR patients'clinical syndromes, insulin sensitivity, glucose and lipid metabolism at least partly through improving the profiles of leptin and adiponectin.