Polycystic ovary syndrome (PCOS) is the commonest endocrine disorder in females in the reproductive period with estimated prevalence of 5% to 18% [1]. It contributes to the mortality and morbidity in patients with PCOS due to the increased risk of different metabolic and cardiovascular (CV) complications [2]. Despite the presence of obesity in 40-60% of cases [3], the disease may occur in non-obese women. The occurrence of metabolic disorders in non-obese PCOS patients, suggests that the syndrome itself may play a role in the development of metabolic and CV co-morbidities [4]. The identification of early stages of atherosclerosis in patients with PCOS might be useful in the development of new strategies to control modifiable CV risk factors [5]. Assessment of vascular endothelial function (ED) as an initial reversible step in atherosclerosis development, may serve as an integral index for CV risk factor burden [6]. In addition, carotid intima media thickness (CIMT) is a helpful marker for atherosclerosis and for the identification of increased risk of CV disease [7]. Our study assessed the early vascular changes in Egyptian women with PCOS both physically and functionally by looking at the CIMT using high resolution Doppler ultrasound and by measuring ED using brachial artery flow–mediated vasodilatation (FMD). Our results indicate that patients with PCOS have significant ED and premature atherosclerosis which is, to a great extent, independent of obesity and IR. This suggests that PCOS patients are at increased risk for premature CVD and may benefit from early detection and management.