Inflammatory bowel disease in childhood has become the subject of intense scientific debate during the last two decades, when there has been a significant rise in its incidence. There is a commonly agreed view that the disorder in children has peculiarities both in terms of underlying mechanisms and clinical management. This review highlights the emerging pathophysiologic concepts and clinical issues in paediatric inflammatory bowel disease and their effects on the management of children with this disorder are discussed. Particular emphasis is given to the link between the improvement of the research in the pathogenetic mechanisms and the development of novel therapeutic strategies able to promote a change in the natural course of the disorder.