Transaldolase is a target of autoimmunity mediated by T cells and antibody (Ab) in patients with multiple sclerosis. Functional T-cell assays, T- and B-cell epitope mapping, and detection of transaldolase-specific antibodies in patients with multiple sclerosis are described. Recombinant transaldolase was produced in a prokaryotic expression vector for use in Western blot analysis of sera of these patients. Overlapping transaldolase peptides 15 amino acids (aa) long were synthesized onto cellulose membranes to map immunodominant B-cell epitopes. Amino acid sequence homologies between viral peptides and immunodominant B-cell epitopes of transaldolase were identified using a computer-based algorithm. Direct assessment of molecular mimicry between transaldolase B-cell epitopes and related viral peptides is also shown. T-cell epitopes are mapped in a T-cell proliferation assay using multiple sclerosis patient and control donor cells. Autoantigen-specific T cells are identified by MHC-peptide tetramer staining using flow cytometry analysis.