The pathogenesis of polycystic ovary syndrome (PCOS) and obesity is not clarified yet. But some parameters such as neuropeptide Y (NPY), angiopoietin-like protein (Angptl-4), omentin-1 are thought to be involved in this pathogenesis. In this study, we aimed to show possible effects of NPY, Angptl-4, omentin-1 throughout clinical parameters and hormones. Patients were divided into three groups. Group I; healthy volunteers, Group II; non-obese women with PCOS and group III; obese women with PCOS. Serum NPY, Angptl-4, free testosterone, total testosterone, luteinize hormone, sex hormone binding globulin, estradiol, dehydroepiandrosterone sulfate, androstenedione, triglycerides and low density lipoprotein cholesterol levels and HOMA-IR, Ferriman-Galwey scores were significantly higher in group II when compared with group I and similarly in group III when compared with group II (p<0.005). While comparing all PCOS patients (obese+non-obese) with healthy volunteers, omentin-1 and high density lipoprotein cholesterol levels were significantly low in PCOS group (p<0.005). As a result of this study, both in the obese and non-obese PCOS patients, there was a significant increase in levels of NPY and Angptl-4 and a significant decline in omentin-1 when compared to healthy subjects. In conclusion, insulin resistance in PCOS patients may be related to the differences of NPY, Angptl-4 and omentin-1 levels and the effects of these differences on metabolic pathways.