The clinical significance of the presence of Clostridium difficile in children's faeces remains uncertain using current diagnostic procedures. Clostridium difficile is a relatively common finding in infants with no symptoms of gastrointestinal disease, suggesting it may be an incidental finding and form part of the normal gut micro-flora in this age group. On the other hand, particularly in older children or those with significant co-morbidity, there are examples where C. difficile causes disease and exerts considerable morbidity and even mortality (C. difficile infection, CDI). Between these extremes lie a substantial group of children who have both diarrhoea and C. difficile in their stools but where the nature of the association is not clear: Clostridium difficile associated disease (CDAD). We review the significance of C. difficile in children presenting recently uncovered paediatric data from a large UK epidemiological study that informs some key unanswered questions.