Some MHC class II genes provide dominant resistance to certain autoimmune diseases via mechanisms that remain unclear. We have shown that thymocytes bearing a highly diabetogenic, IA g7-restricted β-cell-reactive TCR (4.1-TCR) undergo negative selection in diabetes-resistant H-2 g7/x mice by engaging several different antidiabetogenic MHC class II molecules on thymic (but not peripheral) hemopoietic cells, independently of endogenous superantigens. Here we have investigated 1) whether this TCR can also engage protective MHC class II molecules (IA b) on cortical thymic epithelial cells in the absence of diabetogenic (IA g7) molecules, and 2) whether deletion of 4.1-CD4+ thymocytes in IA b-expressing mice might result from the ability of IA b molecules to present the target β-cell autoantigen of the 4.1-TCR. We show that, unlike IA g7 molecules, IA b molecules can restrict neither the positive selection of 4.1-CD4+ thymocytes in the thymic cortex nor the presentation of their target autoantigen in the periphery. Deletion of 4.1-CD4+ thymocytes by IA b molecules in the thymic medulla, however, is a peptide-specific process, since it can be triggered by hemopoietic cells expressing heterogeneous peptide/IA b complexes, but not by hemopoietic cells expressing single peptide/IA b complexes. Thus, unlike MHC-autoreactive or alloreactive TCRs, which can engage deleting MHC molecules in the thymic cortex, thymic medulla, and peripheral APCs, the 4.1-TCR can only engage deleting MHC molecules (IA b) in the thymic medulla. We therefore conclude that this form of MHC-induced protection from diabetes is based on the presentation of an anatomically restricted, nonautoantigenic peptide to highly diabetogenic thymocytes.