The duodenal microflora was studied during the first week of diarrhoea in 40 infants with acute infectious diarrhoea of different aetiologies and compared with that in a convalescent group and a group in whom diarrhoea of known aetiology had persisted for more than 14 days after an acute onset. In the acute phase 16 of the 40 infants had more than 104 colony forming bacteria/ml, predominantly upper respiratory commensals. In over half of the infants infected with enteropathogenic Escherichia coli a faecal type flora was found in the duodenum. This flora included the enteropathogenic E coli serotype isolated from the stool in three quarters of cases. Infants with persisting diarrhoea had significantly more faecal type bacteria in the duodenum than either those with acute diarrhoea or the convalescent group. In addition, there was a significant further increase in Enterobacteriaceae in infants whose persistent diarrhoea occurred after infection with enteropathogenic E coli. Infections with enteropathogenic E coli may have a predilection for disturbing the duodenal microflora, which may contribute to the development of persistent diarrhoea. © 1986, British Medical Journal Publishing Group. All rights reserved.