Forty-nine HIV-infected patients were submitted to peroral jejunal biopsy in order to evaluate the presence of microorganisms and the histomorphometric aspects of the enteric mucosa with subsequent correlation of these findings to the appropriate clinical stage of the disease. Thirty-seven patients fulfilled the CDC criteria for AIDS, of whom 23 presented with diarrhea. Of the 12 patients who had not yet been given an AIDS diagnosis. 3 had persistent generalized lymphadenopathy and 9 were asymptomatic carriers. Flat mucosa was observed in two patients (8.7%) with diarrhea and coccidea. Subtotal villous atrophy and severe lamina propria (LP) mononuclear infiltrate (13%) were found only in patients with diarrhea. Moderate to severe histologic changes were more frequently observed in this group, not always related to the presence of microorganisms. Crypt hyperregeneration was a constant finding. Intraepithelial lymphocyte (IEL) count was decreased in patients with diarrhea. Specific infectious agents were unexpectedly rare for the tropical developing country population studied. The organism most commonly associated with diarrhea was Cryptosporidium sp. (21.7%). The etiology of diarrhea in a significant number of patients remains unclear.