Enteric infections, chronic diarrhea frequently with no obvious etiology, and weight loss cause major morbidity and mortality in acquired immune deficiency syndrome (AIDS). Alterations in mucosal immunity may explain the increased incidence of enteric infections, and contamination of the upper small intestine with bacteria may be the cause of weight loss observed in these patients. To test this hypothesis we studied the mucosal T lymphocyte subset in duodenal mucosal biopsies in 14 AIDS and seven control patients. Duodenal fluid was also cultured for aerobic and anaerobic bacteria. There was a significant decrease among leu-3a T cells (helper/inducer) subset in AIDS. The proportion of mucosal T cells reacting with leu-2a (cytotoxic/suppressor) was significantly increased in AIDS patients. These patients also had a significant reversal of the normal mucosal helper/suppressor T cell ratio. There was no change in the number of leu-7 cells (cells mediate natural killer and antibody-dependent cellular cytotoxicity) as compared to controls. All patients with diarrhea and three of five patients without diarrhea had bacteria in their duodenal fluid. Mean number of organisms was 4.5 X 10(4)/ml. Cultures were negative in all control subjects. The results reveal that the abnormalities of T cell subpopulation in the blood of AIDS patients also occur in their duodenal mucosa. This immunological abnormality is associated with the bacterial colonization of upper gastrointestinal tract which may explain the diarrhea and weight loss observed in majority of our patients. The results also indicate that increased incidence of enteric infections in AIDS may be explained on the basis of altered mucosal immunity.