Autoantibodies can be detected in autoimmune diseases with a long prodromal phase and may serve as early indicators of disease activity. Autoantibody-based screening methods are therefore potent tools for the identification of target antigens. The SEREX method (serological identification of antigens by recombinant expression cloning) has been developed for the serological definition of immunogenic tumor antigens. Recent studies indicate that the SEREX approach may also be utilized for the analysis of complex immune responses involved in autoimmune diseases.