The endothelium is not merely a barrier but it plays a key role in the maintenance of vascular homeostasis. An alteration of the endothelial function (EF) is an early marker of atherosclerosis, also contributing to the development of atherosclerotic lesions and later clinical complications. Systemic autoimmune diseases are characterized by the occurrence of premature atherosclerosis and cardiovascular disease. In view of the prognostic significance of EF for the development of atherosclerotic disease, many studies have evaluated the endothelium in systemic autoimmune diseases, using different techniques. The aim of the present paper is to review the different available techniques to study EF, their advantages and limitations and the data available on the study of EF in systemic autoimmune diseases. Vascular reactivity tests represent the most widely used methods in the clinical assessment of endothelial function. Several techniques were developed to study microcirculation (resistance arteries and arterioles) and macrocirculation (conduit arteries). Studies assessing microvasculature in systemic autoimmune diseases have shown the presence of reduced endothelium dependent vasodilation, while no agreement exists on the presence of endothelium independent alterations. Flow mediated dilation (FMD) has been widely used to evaluate endothelium-dependent vasodilation in peripheral macrocirculation. The majority of studies in systemic autoimmune diseases have shown a decreased brachial artery FMD, whereas endothelium-independent response appears unaffected by the disease in this district. These data strongly underline the different information that could be obtained by different techniques and suggests their combined use in prospective cohorts. Circulating markers of EF include direct products of endothelial cells that change when the endothelium is activated, such as measures of NO biology, inflammatory cytokines, adhesion molecules, as well as markers of endothelial damage and repair. Many of these circulating markers are difficult to measure and quite expensive, and currently are only used in research settings. In view of the complexities in the evaluation of EF, results represent the interaction of several endothelial pathways. No single test currently available is specific for the vascular district tested or the risk factor/diseases considered, and a panel of several tests is therefore needed to characterize the multiple aspects of endothelial biology.