During 17 months, 73 HIV-positive patients with diarrhea lasting at least for 14 days, were studied prospectively. The patients had stool specimen examinations negative for enteric pathogens, or positive for one of them, but with no response to specific treatment. All patients were subcomitted to digestive endoscopy and biopsies were taken for microbiological and histological studies. The etiology of the diarrhea could be established in 48 patients (66%). In 45, the cause was an enteric infection. There was association of 2 pathogens in 11 patients, and of 3 in 1 patient. The agents found were: Cryptosporidium (24%), MAI (16%), Giardia lambila (12%), isospora belli (5%), Shigella (5%), Salmonella (5%); Entamoeba histolytica (3%), HSV (3%), tuberculosis (2%), adherent bacteria (2%) and spirochetes (2%). In 3 patients the etiology was not infection, their diagnoses were coeliac disease, lymphoma and idiophatic colonic ulcers, respectively. In 51% of the cases only the examination of endoscopic biopsy specimens could identify the cause of the diarrhea. These results justify the use of these methods to improve diagnosis and therapeutic attempts in these patients.