The duodenal juice and fecal aerobic microflora was investigated in 54 patients with persistent diarrhea (age less than or equal to 2 years). The duodenal aspirates yielded increased aerobic bacteria (greater than 10(5) organisms/ml) in 28 (51.9%) of the patients. Established enteric pathogens were isolated from the duodenal aspirates of 12 (22.2%) of the 54 patients, viz., enteroadherent Escherichia coli (EAEC) (5), enterotoxigenic E. coli (ETEC) (3), enteropathogenic E. coli (EPEC) (1), nontyphoidal Salmonella (1), and Giardia lamblia (2). The total aerobic bacterial count was greater than 10(5) in all 12 patients positive for specific pathogens apart from one case in whom E. coli showing diffuse adherence to HEp-2 cells were identified. Among the remaining 42 specific pathogen-negative patients, 19 (45.2%) also had greater than 10(5) aerobic organisms/ml in the small bowel. Eight strains of Klebsiella from four of the patients were negative for enterotoxin production in a rabbit ileal loop assay and for adherence to HEp-2 cells. In contrast, 28/54 (51.9%) of the same patients had known enteric pathogens in their stools, viz., nontyphoidal Salmonella (8 or 14.8%), Shigella (2 or 3.7%), Campylobacter (1 or 1.9%), ETEC (4 or 7.4%), EPEC (2 or 3.7%), EAEC (7 or 13.0%), and G. lamblia and Entameba histolytica (3 or 5.6%). Further search for potential virulence factors among aerobic bacteria colonizing the upper small intestine in persistent diarrhea is warranted.