Five children with the acquired immunodeficiency syndrome (AIDS) and unusual gastrointestinal disease are described. Two children presented with malnutrition, abdominal distention, and diarrhea. One was found to have moderately severe villus atrophy on jejunal biopsy and was initially thought to have celiac disease. Jejunal biopsy from the second child revealed infiltration of the mucosa with acid-fast bacilli-laden macrophages. A third child suffered recurrent abdominal pain, progressive weight loss, diarrhea, and severe gastrointestinal hemorrhage secondary to infection with cytomegalovirus. Pseudomembranous necrotizing jejunitis associated with overgrowth of Klebsiella pneumoniae in the duodenal fluid occurred in one patient. The fifth child presented in the newborn period with Serratia marcescens cholecystitis. Gastrointestinal disease in children with AIDS may be due to idiopathic villus atrophy and bacterial or opportunistic infection.