The identification of disease related autoantigens targeted by pathogenic T- and B-cell responses is crucial for the development of improved therapies for autoimmune diseases. To identify immunogenic targets recognized by the humoral immune response, we have recently applied a novel and powerful molecular approach, named ‘serological antigen selection’ (SAS). This method involves the display of a cDNA expression library on filamentous phage and subsequent selection on patient immunoglobulin G (IgG). In the present study, we have cloned a cDNA repertoire from a multiple sclerosis (MS) patient in pVI phage display vectors and performed selections on pooled MS cerebrospinal fluid (CSF) samples immobilized with anti-human IgG. To further streamline this procedure, we report an optimized SAS procedure in which we have successfully established methods for enrichment of MS-specific candidate antigens. In conclusion, the broad applicability of the SAS method makes it a highly promising method for investigating the autoimmune repertoire.