It is currently thought that T cells with specificity for self-peptide/ MHC (pMHC) ligands are deleted during thymic development, thereby preventing autoimmunity. In the case of CD4 + T cells, what is unclear is the extent to which self-peptide/MHC class II (pMHCII)-specific T cells are deleted or become Foxp3 + regulatory T cells. We addressed this issue by characterizing a natural polyclonal pMHCII-specific CD4 + T-cell population in mice that either lacked or expressed the relevant antigen in a ubiquitous pattern. Mice expressing the antigen contained one-third the number of pMHCII-specific T cells as mice lacking the antigen, and the remaining cells exhibited low TCR avidity. In mice lacking the antigen, the pMHCII-specific T-cell population was dominated by phenotypically naive Foxp3− cells, but also contained a subset of Foxp3 + regulatory cells. Both Foxp3 − and Foxp3 + pMHCII-specific T-cell numbers were reduced in mice expressing the antigen, but the Foxp3 + subset was more resistant to changes in number and TCR repertoire. Therefore, thymic selection of self-pMHCII-specific CD4 + T cells results in incomplete deletion within the normal polyclonal repertoire, especially among regulatory T cells.ccording to clonal selection theory, self-reactive lymphocytes are deleted during development, thereby ensuring immunological tolerance to self tissues (1). In the case of T cells, this process occurs in the thymus where developing thymocytes with randomly generated T-cell antigen receptor (TCR) specificities are educated on an array of self-peptide/MHC (pMHC) ligands (2). In the simplest form of this model, thymocytes receiving strong TCR signals are deleted, thereby purging the repertoire of any cells with self-pMHC specificity. The significance of this mechanism of central tolerance has been substantiated by studies demonstrating that impairment of antigen presentation in the thymus can lead to autoimmunity (3, 4). Nevertheless, the clonal deletion rule is challenged by the wellknown observation that immunization with certain self-peptides can induce autoimmunity, indicating that at least some responsive self-pMHC-specific T cells routinely exist in the repertoire (5).Another intriguing exception to the clonal deletion rule is presented by regulatory T (Treg) cells, a suppressive subset of CD4 + T cells defined by expression of the Foxp3 transcription factor (6, 7). Whereas some Treg cells are induced from conventional T cells during immune responses (iTreg), most are socalled natural regulatory T (nTreg) cells, which arise directly in the thymus much like naive CD4 + T cells (8). Studies have shown that nTreg cells develop as a consequence of the type of high-affinity TCR-self-pMHCII interaction that was thought to cause clonal deletion (9). Moreover, extensive TCR sequencing studies of Treg and non-Treg populations have indicated that, whereas the specificities of these repertoires overlap, Treg cell specificity is biased toward self-pMHCII ligands (10, 11).These findings lead to the question of why some sel...