The etiology and pathogenesis of persistent diarrhoea is usually multifactorial and sometimes can not be identified. It is necessary to define if an alteration of the enteric microflora is a risk factor that influence the duration of the diarrhoea. 30 infants with acute diarrhoea and 30 with persistent diarrhoea were studied. A sample of duodenal content was taken by a double-lumen tube and processed microbiologically in search for enteric microorganisms, anaerobic and Candida. These results were correlated with the nutritional status, the previous use of Metronidazole and the results of the stool culture. The presence of bacterial overgrowth and the identification of the duodenal microflora is an important factor for the persistence of the diarrhoea. There was a quantitative and qualitative alteration of the duodenal flora in both groups of patients.