Intrathymic injection of Ag induces Ag-specific tolerance in several clinically relevant experimental autoimmune and transplantation models. However, the exact mechanisms of acquired thymic tolerance in vivo remain unclear. We investigated the mechanisms of acquired thymic tolerance in mice that are transgenic for the TCR specific for peptide 323-339 of OVA. Intrathymic injection of OVA leads to apoptosis of thymocytes starting as early as 3 h after injection and persisting up to 7 days. Double positive thymocytes undergo apoptosis earlier than single positive thymocytes, and significantly higher percentages of double positive thymocytes ultimately die as compared with single positive cells. Apoptotic cells show decreased surface expression of CD4. In the periphery, T cells from intrathymically injected animals had suppressed proliferation and IL-2 production to OVA compared with T cells from control Ag-injected mice. We conclude that intrathymic injection of Ag induces apoptosis of immature thymocytes and a subpopulation of mature thymocytes and induces prolonged anergy in peripheral T cells in vivo. Understanding the mechanisms of acquired thymic tolerance may lead to development of novel clinical strategies to prevent autoimmune disease and transplant rejection.