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The upper small intestinal microflora was determined quantitatively and qualitatively in a group of well-nourished diarrhea-free Nigerian children and compared with those of well-nourished children with acute diarrhea and malnourished children with or without diarrhea. Intestinal aspirate was collected by intubation after a 6-h fast. Well-nourished children without diarrhea had flora consisting predominantly of gram-positive cocci. Total bacterial counts were <105 organisms/ml; 18.2% of aspirates were sterile. In contrast, malnourished children with or without diarrhea had a wider microbial spectrum including Entcrobacteriaceae, Bacteroides, and Candida. Total bacterial counts were between 103 and 109 organisms/ml; none were sterile. In both well-nourished and malnourished groups, no significant quantitative bacteriologic differences were found between patients who had diarrhea and those who did not. Candida and Pseudomonas were found more frequently in malnourished patients with diarrhea. In such diarrheal patients, Pseudomonas, Klebsiella, and enteropathogenic Escherichia coli grew as pure isolates in intestinal aspirates and could be detected concomitantly in their stools. These results establish the upper small intestinal flora of well-nourished diarrhea-free Nigerian children, confirm bacterial overgrowth as a feature of malnourished children with or without diarrhea, and suggest that Candida, Pseudomonas, and Klebsiella may account partly for the diarrhea seen in malnourished children.