The aim of our study was to evaluate early markers of atherosclerosis – endothelium-dependent flow-mediated vasodilation (FMD) of the brachial artery and carotid intima – media thickness (CIMT) in women with polycystic ovary syndrome (PCOS). We examined 90 reproductive age PCOS women (mean age 29.1±1.4 years), who were divided into clinical groups depending on the body mass index and presence of metabolic syndrome (MS). The study included also two groups of comparison – 15 women with metabolic syndrome without PCOS and 30 apparently healthy women. We found endothelial dysfunction in 71.1 % of PCOS women. Decrease of FMD was observed 2 times more often in PCOS and MS group than in MS group and 10 times more often than in healthy women of comparable age. Insulin resistance and hyperandrogenemia were found to be independent predictors of endothelial dysfunction. We found increased CIMT values compared to age and sex normogram in 59.0 % of patients in PCOS and MS group and 26.4 % – in PCOS without MS group, in general 34.4 % of women with PCOS had CIMT values ≥ 75th percentile, which indicates their increased cardiovascular risk. In 3 (13.6 %) patients with PCOS and MS we found atherosclerotic plaques of carotid arteries, which refers them to a very high cardiovascular risk group. Correlation analysis found close relationship between CIMT of PCOS women and total cholesterol, systolic blood pressure, LDL cholesterol, waist circumference and HOMA index. The abdominal type of obesity associated with range of metabolic disorders leading to endothelial dysfunction and CIMT increase was most important in causing endothelial dysfunction and CIMT increase.