Transplantation tolerance across H-2D plus IE antigen barriers has been achieved when B10.Thy1.1 (Kb, IAb, IE-, Db; Thy1.1) mice were primed i.v. with 9 x 10(7) spleen cells plus 3 x 10(7) bone marrow cells from B10.A(5R) (Kb, IAb, IEb, Dd; Thy1.2) and treated i.p. with 200 mg/kg of cyclophosphamide (CP) two days later. The tolerant state was confirmed by prolonged acceptance of donor-type skin grafts, and in vitro unresponsiveness to donor antigens. From the early stage of tolerant state, V beta 11+ or V beta 5+ T cells expressing CD4 or CD8 accessory molecules were markedly decreased in the periphery of the tolerant mice. Moreover, neither CD4+CD8- nor CD4-CD8+ thymocytes bearing a high density of V beta 11 or V beta 5 were detected in the chimeric thymus. The intrathymic clonal deletion appeared to be maintained in some of the recipient mice even after the disappearance of detectable mixed chimerism in the late stage. These results suggest that the mechanisms of the CP-induced tolerance include the destruction of the IE (and probably H-2D) reactive T cells in the periphery followed by the intrathymic clonal deletion of T cells reactive against these antigens. These results directly show the strong correlation between transplantation tolerance to H-2 alloantigens and the disappearance of alloreactive T cells in both the periphery and thymus.