Focal crypt epithelial cell degeneration (apoptosis) of the rectum is a characteristic pathologic feature in AIDS. The presence of apoptosis usually implies cell-mediated cytolysis, which would be an unexpected finding in this disease. We investigated the ultrastructural features of apoptosis in rectal biopsies from five AIDS patients (three homosexual males and two females with i.v. drug abuse), three heterosexual controls, and two homosexual male controls. Apoptosis was found in all AIDS patients and, to a lesser extent, in one heterosexual control. Ultrastructurally, vacuolization of several adjacent cells, leading to extrusion of cellular debris through the basal lamina and phagocytosis by macrophages, was seen. No intracellular or extracellular viral particles were detected in the regions containing apoptotic bodies, in epithelial cells near the crypt bases, in intraepithelial lymphocytes, or in macrophages. In summary, apoptosis in the rectal crypts of patients with AIDS has the same ultrastructural features as in other conditions, which suggests that its pathogenesis is related to immune rather than infectious factors. If this process occurs on a chronic basis in multiple cell types, it would promote general tissue depletion, which has been demonstrated to occur in AIDS. The presence of apoptosis in AIDS is not explained by current concepts of disease pathogenesis.