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Patients with chronic constipation that fails to respond to treatment remain a challenge for paediatricians and surgeons. Ongoing work in our institution suggests that a number of children with intractable symptoms have slow transit constipation, which has only been described recently in paediatrics. Common features of slow transit are: delayed passage of the first meconium stool beyond 24 h of age, symptoms of severe constipation within a year, or treatment-resistant 'encopresis' at 2-3 years, soft stools despite infrequent bowel actions, and delay in colonic transit on a transit study. A proportion of children with slow transit constipation have an abnormality of intestinal innervation associated with the dysfunctional colonic motility, recognized as intestinal neuronal dysplasia (IND). Intestinal neuronal dysplasia type B, the most common variant of IND, is defined on rectal biopsy by hyperplasia of the submucosal plexus. On laparoscopic colon muscle biopsy, many specimens show reduced numbers of excitatory substance P-immunoreactive nerve fibres in the circular muscle. Functional markers of the nerves allow new diagnostic criteria to be developed which may also allow a more rational approach to treatment. The aetiology remains obscure and the optimal management poorly defined, although subtotal colectomy, proximal colostomy or appendicostomy (for antegrade enemas) have been tried. Once the anatomy and physiology of the colon in children with slow colonic transit is better understood, we will have defined not only a new form of constipation, but also will be able to consider new therapies.