Enterobacteriaceae isolated from the duodena of Peruvian children with persistent diarrhea (PD) have been examined for virulence factors and compared with Enterobacteriaceae isolated from children with acute diarrhea, those convalescent from PD and diarrhea-free controls. Escherichia coli were isolated from 42 of 186 (23%) of the aspirates. All 11 children with PD in whom multiple E. coli colonies were examined were colonized by a single serotype. DNA probes identified enterotoxigenic E. coli in 2 of 89 (2.2%) PD aspirates and 2 of 38 (5.3%) acute diarrhea aspirates and enteroaggregative E. coli in one PD and one control aspirate. Strains positive with the enteropathogenic E. coli adherence factor probe were identified from 2 of 89 (2.2%) patients with PD and 1 of 34 (2.9%) controls. A subset of 12 E. coli strains failed to show adhesion to human duodenal enterocytes although 5 of 9 showed sparse but polar attachment to ileal cells from a child with short bowel syndrome and PD. Three of 10 Enterobacteriaceae (two E. coli, one Klebsiella species) caused diarrhea in the reversible ileal tie adult rabbit model. Colonization with virulent Enterobacteriaceae did not explain the majority of episodes of PD. Examination of these duodenal bacteria in the rabbit model revealed some that caused diarrhea but were not recognized pathogens.