Injection of TCR transgenic mice with antigenic peptide results in the deletion of immature thymocytes expressing the transgenic TCR. We have analyzed this process in mice transgenic for a TCR (F5) that recognizes a peptide from the influenza nucleoprotein (NP68). To determine whether deletion of immature thymocytes is the result of specific recognition of the antigenic peptide by the thymocytes or mature T cell activation, bone marrow chimeric mice were generated using a mixture of cells from F5 transgenic and nontransgenic mice. Injection of these mice with antigenic peptide leads to the preferential depletion of F5 transgenic thymocytes, whereas nontransgenic thymocytes remain largely unaffected. Furthermore, exposure of F5 fetal thymic lobes to peptide leads to thymocyte deletion even though no mature single positive T cells are present at this stage. These data suggest that Ag-induced death of immature thymocytes is due to peptide-specific recognition, although activated mature T cells appear to potentiate such deletion. Further administration of antigenic peptide to F5 mice results in the appearance of double-positive thymocytes that are resistant to Ag or anti-CD3-induced apoptosis. These data suggest a change in the ability of the cells to signal through the TCR-CD3 complex, resembling the state of anergy induced in peripheral T cells following chronic exposure to Ag.