Anti-endothelial cell antibodies (AECA) are detectable in a heterogenous group of autoimmune and inflammatory conditions. These antibodies have also been detected in healthy individuals. Nevertheless, most of the literature focuses on AECA in pathological conditions and their targets and functions in healthy individuals remain to be clarified. Recently, proteome-based technologies have been successfully used for the identification of antigens targeted by natural AECA. Thus, it has been shown that IgG AECA can be detected in sera from healthy individuals that recognize a restricted set of proteins among a whole protein extract of umbilical vein endothelial cells. These proteins correspond to ubiquitous proteins belonging to highly conserved protein families and exerting pivotal roles in cell physiology, including cytoskeletal proteins (beta actin, vimentin, alpha tubulin) and glycolytic enzymes (glyceraldehyde-3-phosphate-deshydrogenase and alpha-enolase). As reported for other types of natural autoantibodies, natural AECA could exert anti-inflammatory and anti-thrombotic functions. In addition, they could play a role in the control of EC activation.