In patients with cyanotic congenital heart disease, chronic hypoxaemia leads to important changes in blood vessel function and structure. Some of these alterations are maladaptive and probably contribute to impaired cardiopulmonary performance and an increased incidence of thrombotic and embolic events. Recent evidence suggests that deranged endothelial function, a sequel of chronic cyanosis, could be an important factor in the pathogenesis of cyanosis-associated cardiovascular risk. In this article, we discuss the physiological and mechanical consequences of compensatory erythrocytosis and possible pathophysiological mechanisms of vascular dysfunction in chronic cyanosis.