Both direct and indirect antigen presentation lead to deletion of antigen-specific T cells in engrafted mice. 4C (direct pathway, A-D) or TCR75 (indirect pathway, E) fetuses were transplanted with BALB/c fetal liver cells and the percentage of TCR-Tg CD4 cells was compared among chimeras, injected nonchimeras, and uninjected animals. TCR-Tg cells were identified by staining for CD4 and Vβ13 (4C hosts) or Vβ8 (TCR75 hosts). The proportion of TCR-Tg cells was quantified by either the CD4:DP ratio (thymus) or the CD4:CD8 ratio (spleen). Comparisons were made between (A,C,E) cell percentages or (B,D) absolute cell counts. Pearson correlations were used to compare the percentage of TCR-Tg cells and the percentage of chimerism. 4C: uninjected, n = 5; chimera, n = 6; nonchimera, n = 2. TCR 75: uninjected, n = 7; chimera, n = 4; nonchimera, n = 4. P values: *<.05; **<.01; ***<.001; ****<.0001.