Abstract T cell auto- and allo- reactivity is primarily tamed in the periphery by thymus-derived CD4 regulatory T cells (Tregs) that mature in the medullar compartment. We have achieved Treg-dependent tolerance of fully allogeneic transplants via the transfer of donor MHC class II genes (MHCII) that induced newly made Tregs specific of donor MHCII peptides. Given that gene therapy for tolerance was effective with MHCII but not MHCI genes, the goal of the study was to identify natural MHCII peptides able to impact Treg development and function. Using experimental models that either recapitulated MHCII peptide presentation - the IEα 52-68 peptide presented on I-Ab molecules - or promoted Treg-mediated tolerance to heart grafts via MHCII gene transfer, we confirmed that high amounts of IEα peptide were presented by MHCII from most if not all I-Ab+ CD11c+ dendritic cells of the thymic medulla, suggesting its role in Treg maturation. This hypothesis was confirmed by demonstrating that the introduction of the IEα peptide through hematopoietic chimerism converted host IEα-specific CD4 T cells into CD25hiFoxp3+ suppressive Tregs. Treg suppression for tolerance to transplants required prior activation by cognate pMHCII complexes as MHCII-treated recipients rejected MHCII-deficient while accepting MHCII-sufficient grafts. These data are consistent with a prominent role of “MHCII self-presentation” in shaping thymic Treg TCR specificities and controlling Treg function in the periphery.