Susceptibility to type I diabetes is linked to class II MHC alleles in both mouse and man. However, the molecular mechanisms by which MHC molecules mediate disease susceptibility are unknown. To analyze how I-A alleles predispose to, or prevent, the development of type I diabetes, we have chosen, as the first step, to investigate the immune response to an important islet cell protein in diabetes-susceptible and diabetes-resistant mice. MHC class II alleles conferring susceptibility and resistance to diabetes select completely different sets of immunogenic epitopes from the β islet cell autoantigen glutamic acid decarboxylase 65. Peptide-binding studies, analysis of MHC restriction, and immunization with these peptide epitopes indicate that the two amino acid substitutions within the I-A_β chain that distinguish a diabetes-susceptibility from a diabetes-resistance allele are sufficient to alter peptide binding and MHC restriction and may also influence antigen presentation and the selection of the T cell repertoire. The data indicate that the molecular mechanisms for class II-mediated selection of immunodominant epitopes are complex and differ for each individual peptide epitope. Further study of the functional characteristics of the response to these epitopes should provide insight into mechanisms of MHC-mediated diabetes susceptibility.