We compared the fine structure of the biopsied rectal mucosa of seven allogeneic bone marrow transplant recipients who had gastrointestinal graft-versus-host disease (GVHD) with that of four recipients without GVHD. In GVHD, lymphocytes formed the predominant cellular infiltrate. Lymphocytes indented the cytoplasmic membranes of enterocytes by point contact, extended broad pseudopods to the nuclear membranes of the enterocytes, and surrounded desmosomes. The membranes of target cells were never breached, however. We hypothesize that these lymphocyte-to-epithelial-cell contacts represent the recognition phase of alloimmune T-lymphocyte cytolysis. Damage to the enterocytes resulted in both coagulative necrosis and "apoptosis" (the development of membrane-bound cell fragments--"apoptotic bodies"). Epithelial injury and lymphocytic infiltration predominated in the bases of the crypts in mild GVHD and extended to the surface epithelium in severe GVHD. Chemoradiotherapy-induced injury, present early post-transplant, was diffuse and severe but transient. In GVHD, damage to the enterocytes, necrosis, and intercellular edema extended beyond the time of resolution of chemoradiotherapy-induced injuries. Patients without GVHD, studied after resolution of chemoradiation injury, had rectal epithelium with little or no injury and no evidence of either increased numbers of lymphocytes or of the intimate lymphocyte-to-epithelial-cell contacts described in those with GVHD.