Objective: The recommended composition of a hypocaloric diet for obese women with polycystic ovary syndrome (PCOS) is unclear. The aim of this study was to investigate the effects of a high-protein, low-glycemicload diet compared with a conventional hypocaloric diet on reproductive hormones, inflammatory markers, lipids, glucose, and insulin levels in obese women with PCOS. Methods: A total of 60 overweight and obese women with PCOS who did not use insulin-sensitizing agents were recruited and randomly assigned to 1 of the 2 hypocaloric diet groups for a single-blind clinical trial. The groups included a conventional hypocaloric diet (CHCD) (15% of daily energy from protein) and a modified hypocaloric diet (MHCD) with a high-protein, low-glycemic load (30% of daily energy from protein plus lowglycemic-load foods selected from a list) that was prescribed via counseling visits weekly during 12 weeks of study. Anthropometric assessments and biochemical measurements including reproductive hormones, inflammatory factors, lipids, glucose, and insulin were performed on fasting blood samples at baseline and after 12 weeks of dietary intervention. Results: Weight loss was significant and similar in the 2 groups. Mean of testosterone in the MHCD and CHCD groups decreased from 1.78 ± 0.32 to 1.31 ± 0.26 ng/ml and from 1.51 ± 0.12 to 1.15 ± 0.11 ng/ml, respectively (p< 0.001). Follicle sensitizing hormone (FSH), luteinizing hormone (LH), and blood lipids concentrations were not changed except low-density lipoprotein cholesterol (LDL-C) was reduced by 24.5% ± 12.3% (p< 0.001 for both) after 12 weeks of intervention. MHCD resulted in a significant reduction in insulin level, homeostatic model assessment for insulin resistance (HOMA), and high-sensitivity C- reactive protein (hsCRP) concentration (p< 0.001). Conclusions: In this study both hypocaloric diets significantly led to reduced body weight and androgen levels in these two groups of women with PCOS. The combination of high-protein and low-glycemic-load foods in a modified diet caused a significant increase in insulin sensitivity and a decrease in hsCRP level when compared with a conventional diet.