Abstract During thymic development, T cells with specificity to self-antigens are deleted, thereby ensuring that the peripheral repertoire is devoid of potentially autoreactive clones. However, the ultra-low frequency of naive epitope-specific T cells has made the direct test of this theory technically unfeasible in the past. Using peptide:MHC (pMHC) multimers coupled with magnetic bead enrichment, we have directly studied endogenous polyclonal populations of naive CD4+ T cells with specificity for an I-Ab-restricted model antigen, 2W1S, that is foreign in C57BL/6 mice (B6) or self in mice transgenically expressing the model antigen (Act-2W). Act-2W mice contained a population of 2W1S-specific T cells that was about 25% the size of that in B6 mice, demonstrating that thymic deletion of self-antigen specific T cells is incomplete. Nonetheless, these cells were tolerant to 2W1S, as they did not develop autoimmune responses or respond to large doses of exogenous 2W1S antigen administered in vivo. Antigen receptors expressed by these cells exhibited features of reduced pMHC ligand binding affinity, indicating a preferential loss of high-affinity 2W1S-specific clones during thymic selection. Moreover, a greater proportion of 2W1S-specific T cells expressed FoxP3 in Act-2W mice than in B6 counterparts, suggesting that regulatory T cell development may also function as a mechanism of T cell tolerance to self-antigens. This work was funded by NIH grants PO1-AI35296 and F32-AI063793.