Although few episodes of diarrhea last longer than 14 days these episodes are particularly associated with growth faltering and malnutrition. We have examined the role of the duodenal microflora in prolonging diarrhea in Peruvian children ages 3 to 36 months by comparing the microflora in 89 children with persistent diarrhea, 38 children with acute diarrhea and 34 diarrhea-free controls from the same environment. Bacteria were retrieved from 93% of all aspirates, including 94% of those from controls. There were no significant differences among the 3 groups with respect to total bacterial count, to the proportion of children with duodenal Enterobacteriaceae and to the proportion with anaerobes, lending no support to the hypothesis that proliferation of bacteria in the small intestine during the acute illness prolongs diarrhea. When only children older than 18 months were compared, anaerobes were cultured more frequently from those with persistent diarrhea than from controls, but the presence of anaerobes was not associated with adverse clinical outcome. Although malabsorption, especially steatorrhea, was common, there was no association between elevated bacterial counts and fecal loss of nutrients in 69 children who received the same diet. In this population steatorrhea could not be attributed to bacterial overgrowth.