We assessed the kinetics of V beta 6+ T cell elimination in the lymph nodes and thymus during Mls-1a mouse ontogeny. Our results suggest that induction of tolerance to Mls-1a antigens involves mechanisms other than clonal deletion of immature T cells in the thymus. Mature CD4+CD8- (CD4SP) T cells were affected by Mls-1a antigens earlier than immature thymocyte populations. Up to 2 weeks after birth, reduced frequencies of V beta 6+ T cells were detected only in CD4SP cells from the thymus and lymph nodes, and generation of CD4SP cells in the thymus was blocked at least 1 week earlier than that of their CD4+CD8loTCRhi immature precursors. The number of V beta 6+CD4SP T cells increased during the first 2 weeks of life and remained constant thereafter. We thus found no evidence of deletion of mature V beta 6+CD4SP T cells, as the reduced frequencies in adult mice can be attributed to the dilution of previously generated cells in lymphoid organs of growing mice, which increase in cellularity after birth. V beta 6+CD4+ T cells were activated in vivo shortly after birth, as shown by a selective increase in IL-2 receptor alpha chain expression in the thymus and lymph nodes from day 0 to day 2 after birth. It is therefore likely that endogenous expression of Mls-1a antigen shortly after birth activates V beta 6+CD4SP T cells and renders them anergic. This process of tolerance induction may precede the clonal deletion of immature T cells in the thymus, described in the adult mouse.