The invention provides methods for identifying peptide epitopes that activateCD4+ T cells involved in the pathogenesis of diseases, e.g., autoimmunediseases, susceptibility to which is determined by expression of particularclass II MHC genes. The invention includes peptides derived from the IA-2polypeptide by such a method, altered peptide ligands, and methods of therapyinvolving the use of altered peptide ligands.