Commonly available information on intestinal neuronal dysplasia (IND) is sparse. Especially well documented long-term courses are lacking. The aim of this study was to correlate defecation as a clinical parameter of the long-term course in malformations of the enteric nervous system with the morphological diagnosis. 57 children with intestinal neuronal dysplasia (IND) or aganglionosis with cranial intestinal dysganglionosis (agIND), diagnosed between 1983 and 1992, were analysed including histomorphological classification, collection of clinical data and evaluation of the defecation mode by questionnaire as a parameter of the long-term course. Of 29 dysganglionic (IND) patients, 9/29 cases (31 %) had been treated conservatively, 18/29 cases surgically (62.1%), in two children (6.9%) no therapy had been necessary. All 28 patients with Hirschsprung's disease and cranial IND (agIND) underwent resection. 46 of the children could be followed up 3.64 years after the end of the main therapeutic period and with a mean age of 6.7 years at the time of follow-up; 43.5% of the analysed children still showed severe constipation. 23.9% only were really cured; 15.2% had normal defecation still using conservative treatment and 17.4% had diarrhea. No significant difference was found between both groups, IND and agIND, and the results were independent of treatment modality. The results were much worse than in idiopathic constipation as reported in the literature and even worse in comparison to unselected Hirschsprung collectives. It has to be concluded that in IND with chronic constipation intensive long-term care is necessary and it is crucial that treatment algorithms should be outlined urgently together by pediatric gastroenterologists and pediatric surgeons. AgIND seems to need more extended resection following an exact histomorphological mapping by biopsies taken during enterostomy procedure.