The postnatal ontogeny of potentially autoreactive T cells has been studied in a model system where a particular TCR beta chain variable domain (V beta 6) is correlated with reactivity to a minor antigen encoded by the Mlsa locus. Although absent among mature (CD4+ or CD8+) T cells in adult mice expressing Mlsa, brightly staining V beta 6+ cells were readily detectable in the thymus of neonatal animals, reaching a maximum after 4 d and decreasing rapidly thereafter. These V beta 6+ thymocytes were predominantly of the CD4+ phenotype and were localized in the medulla of the developing thymus. Furthermore, the intensity of TCR expression by these CD4+ cells was significantly (twofold) reduced as compared with age-matched Mlsb controls. A rapid disappearance of CD4+V beta 6+ cells (and corresponding decrease in TCR density) could also be observed in the thymus of Mlsb mice that had been injected neonatally with Mlsa spleen cells. Taken together, these results raise the possibility that some autoreactive T cells may persist after birth and that TCR downregulation may occur as a physiological response to tolerogenic signals in vivo.