According to some studies, polycystic ovarian syndrome (PCOS) patients have an increased risk for diabetes mellitus and often show an adverse cardiovascular risk profile. NT-proBNP was shown to have a high predictive value regarding cardiovascular events, especially in those without overt cardiovascular disease. The aim of this study was to investigate the levels of NT-proBNP in 70 women with PCOS and/or obesity in relation to other classical cardiovascular risk factors. There was no statistical difference between NT-proBNP levels between obese, lean PCOS and obese PCOS patients; between patients with or without metabolic syndrome; or between patients with different cardiovascular risk, according to The Androgen Excess and PCOS Society consensus. NT-proBNP does not show significant correlation to age, weight, BMI, WHR, WSR, systolic or diastolic blood pressure and results from oral glucose tolerance test (OGTT), except for immunoreactive insulin (IRI) at 120 min. NT-proBNP correlates weakly with HDL, but not with other indices of lipid metabolism.