The role of Clostridium difficile in the aetiology of diarrhoea in children with Hirschsprung's disease was investigated in a prospective longitudinal study. In 64 children with Hirschsprung's disease no significant difference was found in the isolation rate of C difficile in patients with diarrhoea (32%) and without diarrhoea (26%). Comparable isolation rates were found in 47 control children with and without diarrhoea (27% and 16% respectively). The number of strains producing toxin B was similar in the four groups of children. In contrast to the disappearance of C difficile by 12 months of age in the control groups of children, C difficile could be repeatedly isolated from a proportion of children with Hirschsprung's disease over 12 months of age. These findings help to reconcile the existing contradictory reports on the incidence of C difficile in Hirschsprung's disease associated enterocolitis.