Human immunodeficiency virus (HIV)-associated intestinal abnormalities can occur before immunodeficiency or infection with opportunistic enteropathogens. Rhesus macaques infected with simian immunodeficiency virus (SIV) develop an AIDS-like illness that frequently includes enteropathy. The development of enteropathy and its association with SIV infection in the intestinal tract was examined. By 1 week after infection, SIV-infected macrophages and T lymphocytes were detected in gut-associated lymphoid tissue. In contrast to findings in the asymptomatic stage, SIV-infected macrophages were numerous in primary and terminal stages of infection. An acute enteropathy syndrome was observed in the primary acute stage of infection. Functional abnormalities of absorptive epithelium, indicated by D-xylose malabsorption and decreased sucrase activity, occurred before the onset of diarrhea or opportunistic enteric infections. These findings indicate that macrophages and T cells in the intestinal tract are early targets of SIV infection and may play a critical role in the development of SIV-associated intestinal dysfunction.