The aim of this study is to investigate the correlations between the serum levels of obestatin and copeptin, carotid artery intima-media thickness (CIMT), and brachial artery flow mediated dilatation (FMD) in obese and non-obese women with PCOS. Secondly to investigate their relationship with each other and with clinical, metabolic, hormonal parameters and cardiovascular risk factors. We analyzed 54 patients with PCOS and 20 age-matched healthy women as controls. PCOS patients were divided into two groups based on body mass index (BMI): obese group (BMI > 30 kg/m2, n = 28) and non-obese group (BMI < 30 kg/m2, n = 26). Serum copeptin and obestatin levels, insulin homeostasis model assessment for insulin resistance (HOMA-IR), CIMT and brachial artery FMD were determined and compared among the groups. Women with PCOS, especially obese ones, had higher triglycerides, HOMA-IR, hirsutism score, total testosterone, CRP, systolic and diastolic blood pressure, and waist-to-hip ratio (WHR), and lower HDL. Serum obestatin levels were significantly lower in obese PCOS group than non-obese and control. While Serum copeptin levels were significantly higher in obese PCOS group than non-obese and control. Brachial artery FMD was lower in the PCOS groups than control. Obestatin was positively correlated with cardiovascular risk factor (FMD), whereas copeptin was negatively correlated with FMD. Obestatin and copeptin may provide useful information regarding future cardiovascular risk in PCOS patients as obestatin was negatively correlated and copeptin was positively correlated with cardiovascular risk factor (FMD).