Diarrhea, the etiology of which often is obscure, is a major complication of human immunodeficiency virus (HIV) disease. Diarrheogenic bacterial infections (eg, enteropathogenic Escherichia coli) are diagnosed traditionally by stool analysis rather than by examination of endoscopic biopsy specimens. Although E coli rarely have been associated with diarrhea in HIV/acquired immunodeficiency syndrome (AIDS) patients, neither have they routinely been sought. Endoscopic ileal and colorectal biopsy specimens from AIDS-positive patients with chronic diarrhea were analyzed by light and transmission electron microscopy (TEM). The surface epithelium of many large intestinal biopsy specimens previously diagnosed with, for example, nonspecific colitis, regularly showed disarray, degeneration, and necrosis, often with polymorphonuclear neutrophils (PMNs) and eosinophils, irregular cell aggregates, cell shedding, and defects. The crypts were not involved nor were consistent changes noted in the lamina propria. Closer scrutiny of 52 of these biopsy specimens showed gram-negative coliform bacteria intimately associated with histopathology in four distinct patterns. In 22 biopsy specimens, including two from infants, four morphological types of bacilli were observed that adhered to and effaced the brush border in the classic manner with cytoskeletal rearrangement and pedestals. Other bacterial morphologies and/or patterns of epithelial interaction also were observed (ie, thin bacilli intercalated between microvilli [n = 7], loosely associated bacilli [n = 21], and enterocyte invasion by long rods [n = 2]). Three patients also had minor ileal involvement. Infection was greatest in the right colon and coinfections (eg, microsporidia, Mycobacterium avium complex, adenovirus, and especially cytomegalovirus) were documented in 37% (19 of 52) of specimens. Diarrheogenic bacterial infections, some of the E coli type, may be an important cause of diarrhea in HIV disease. Their precise characterization is needed so that stool samples, not endoscopic biopsy specimens, can be used for diagnosis.