Cutaneous and mucosal epithelial cells are primary targets of injury in acute graft-versus-host disease (GVHD), the principal complication of allogeneic bone marrow transplantation. Recent experimental data in skin suggest that early lesions may precede morphologic evidence of direct infiltration by effector cells. The purpose of this study was to further elucidate the mechanism and kinetics of epithelial injury in acute GVHD produced in mouse strains (B10.BR/CBA) receiving bone marrow transplants across minor histocompatibility loci. Skin and tongue mucosa of hosts receiving CD8 T-cell–enriched, whole T-cell–enriched, or T-cell–depleted bone marrow transplants were sequentially harvested and studied histologically and by the terminal uridine deoxynucleotidyl transferase end ligation technique to detect apoptotic cells. Apoptosis involving putative stem cells is the predominant form of cellular injury in acute experimental GVHD. Although apoptosis correlated with the onset of lymphocyte infiltration relatively late in CD8-mediated disease, apoptosis was bimodal in whole T-cell–mediated disease, with an early peak that preceded histologic evidence of lymphocyte infiltration. These findings establish a central role for apoptosis in epithelial cell injury in acute GVHD and indicate that T–cell composition of the donor marrow inoculum may influence the pattern and kinetics of epithelial damage.