Autoimmune diseases such as rheumatoid arthritis (RA) are characterized by autoantibodies to different autoantigenic proteins. Using proteomic 2D immunoblots, we identified a new 40 kDa autoantigen – hnRNP A3 – from HeLa nuclear extracts, which is frequently (30%) detected by RA. Moreover, we used a set of protein arrays of about 50 000 proteins derived from a human foetal brain cDNA expression library for screening with patient sera. Additionally, we utilized a human foetal brain cDNA library in a robot-based T7 phage display screening system with RA patient sera. To determine the diversity of the enriched library, we amplified the cDNA inserts and hybridized them onto the custom-made human ENSEMBL cDNA array. By these methods, over 80 clones were identified to bind patient immunoglobulins. Moreover, nine clones show only IgA-specific reactivity. We have now evaluated two different clones thoroughly: the carboxyl-terminal half of the nucleolar phosphoprotein p130 (NOPP 130) and a clone representing a 41-amino-acid mimetic peptide showing homology to calreticulin, a previously reported autoantigen. The remaining proteins are still undergoing thorough investigation. Applying state-of-the-art proteomic techniques, such as protein array and phage display, we have succeeded in identifying more than 80 potentially autoantigenic marker molecules, of which we have characterized a subset for RA specificity by screening with large numbers of patient and control sera. However, none of the molecules characterized thus far is exclusively discriminatory for RA and they all exhibit overlap with other autoimmune diseases.