A prospective study was designed to investigate the causes of chronic diarrhea in AIDS patients in Thailand. Forty-five patients from Bamrasnaradura Infectious Diseases Hospital were enrolled. Extensive investigations included multiple stool examinations for ova and parasites, using the stool formalin-ether concentration method, stool culture, stool acid-fast bacilli (AFB) stain, stool modified AFB stain, esophagogastroduoscopy with duodenal aspirate and biopsy, and colonoscopy with biopsy. Biopsied specimens were examined with H&E, Giemsa, Gram, Periodic acid Schiff, and AFB stains. Definitive causes were found in 29 patients (64.4%). Of these 29, 7 patients were found to habor more than 1 pathogen (15.5%). The most commonly found enteric pathogen was Cryptosporidium parvum (20.0%). Less frequently found pathogens were Mycobacterium tuberculosis (17.8%), Salmonella spp. (15.5%), Cytomegalovirus (11.1%), Mycobacterium avium intracellulare (6.6%), Strongyloides stercoralis (4.4%), Giardia lamblia (4.4%), Cryptococcus neoformans (2.2%), Histoplasma capsulatum (2.2%), Campylobacter jejun (2.2%), and Cyclospora cayetanensis (2.2%). Salmonella spp., Mycobacterium tuberculosis, and Mycobacterium avium intracellulare infections were shown to be more common in Thailand than in African countries.