Since the first description of self-reactive antibodies in systemic autoimmune rheumatic diseases, many autoantigens have been identified as useful diagnostic biomarkers in clinical immunology. Among the autoantigens, double-stranded desoxoribonucleic acid (dsDNA), the Smith antigen (Sm), topoisomerase-I (topo-I), proliferating cell nuclear antigen (PCNA), and others were described as hallmark targets of systemic autoimmune diseases. The detection of the corresponding autoantibodies can be performed with a variety of immunoassays based on native antigens, recombinant proteins or synthetic peptides. As discussed in this review, synthetic peptides often represent highly accurate antigenic ligands for autoantibody assays that can be easily produced in high quality and quantity and with remarkable reproducibility. Furthermore, the use of peptides that focus on abrogation or neutralization of pathogenic autoantibodies provides a possible new therapeutic approach to the management of autoimmune disorders. There is an increasing number of interesting examples for the application of synthetic peptides in diagnostic approaches. Todays sophisticated epitope mapping methods will potentate the identification of further peptides that can be possibly used as specific targets in diagnostic and therapeutic approaches to improve the patients treatment. This may lead to a new scientific research area with high impact on the development of diagnostic and therapeutic products, to the area of peptide engineering and “theranostics”.