In flow microfluorometry analysis of thymus and lymph node cells of C57BL/6(I-E-,Mlsb) mice rendered neonatally tolerant to (C57BL/6 x AKR/J)F1 (I-E+,Mlsb/a) lymphoid cells, both CD4+ and CD8+ cells showed a striking reduction in the number of V beta 6+ cells capable of recognizing Mlsa in the context of major histocompatibility complex (MHC) class II molecules, indicating that clonal deletion of V beta 6+ cells by Mlsa antigen occurs just at a stage of immature V beta 6lowCD4+CD8+ thymocytes. On the other hand, the number of V beta 11+ cells capable of recognizing I-E was markedly reduced in CD4+ cells, but CD8+ cells showed only partial (20%) reduction of such a population. The clonal deletion of V beta 11+ cells by I-E may begin at the transitional stage from V beta 11lowCD4+CD8+ to V beta 11highCD4+CD8- single-position cells, and V beta 11lowCD4+CD8+ cells differentiating to V beta 11highCD4-CD8+ cells seem to be resistant to clonal deletion. V beta 11+ T cells are also stimulated by staphylococcal enterotoxin A (SEA) irrespective of expression of CD4 or CD8. Nearly all of both V beta 11+CD4+ and V beta 11+CD8+ lymph node T cells were deleted by the injection of SEA every other day from birth. In their thymi, both V beta 11+CD4+CD8- and V beta 11+CD4-CD8+ single-positive thymocytes were deleted, and the proportion of V beta 11low thymocytes was lower than that of normal mice. The clonal deletion of V beta 11+ T cells by SEA injection occurs at a stage of immature V beta 11lowCD4+CD8+ double-positive thymocytes, resulting in deletion of both V beta 11+CD4+ and V beta 11+CD8+ T cells.