Screening a cDNA expression library is a powerful technique that allows identification of previously uncharacterized antigens. Proteins recognized by antibodies from patients with autoimmune diseases have been intensively studied over the past two decades since cDNAs encoding autoantigens have become available. Identity of many of them has been defined, and specific structural motifs or post-translational modifications, which may be important to explain the generation of such antibodies during the autoimmune process, have been pointed out. The screening of human umbilical artery or microvascular endothelial cell expression libraries appears to be a useful tool for the characterization of endothelial autoantigens allowing us to identify several molecules recognized from serum anti-endothelial cell antibodies of patients with diseases characterized by immune-mediated endothelial dysfunctions. © 2007 New York Academy of Sciences.