Chronic inflammatory and infectious diseases of the central nervous system (CNS) are characterized by increased IgG and oligoclonal bands (OGBs) in the brain and cerebrospinal fluid (CSF). The OGBs in CNS infectious diseases of known cause have been shown to be directed against the pathogenic agent. In multiple sclerosis (MS), the antigenic specificity of the OGBs is unknown, but could be directed against an infectious agent, an autoantigen, or both. In a molecular approach to identify antigens specific for MS, we constructed directional cDNA expression libraries with mRNA extracted from chronic and acute MS plaques and periplaque white matter. The libraries were: (1) screened to identify clones whose expression products react with MS CSF, but not with CSF from other infectious and inflammatory diseases of the CNS; (2) subtracted by hybridization to mRNA from normal human brain white matter and differentially screened to detect unique MS transcripts; and (3) used as template in polymerase chain reactions to amplify, clone, and sequence IgG heavy and light chain variable regions (VH and VL, respectively) expressed in MS plaques. Analysis of the VH and VL IgG repertoire in MS brain may identify disease-relevant IgG sequences that can be assembled into functional antibodies using recombinant phage technology. Such recombinant antibodies will be useful to probe brain tissue to identify antigens unique to MS.