A total of 106 consecutive children with intestinal neuronal malformations were included in a prospective study. The intestinal transit time was assessed using a modification of Hinton's method. The results of transit time studies, the associated specific histochemical findings, therapeutic procedures, and the clinical course on follow-up assessments over a mean period of 2.4 years were analysed. The intestinal transit time was prolonged in all 53 patients with aganglionosis and in 37 (69.8%) out of 53 children with other intestinal malformations. Eight out of 16 children with IND type B had an abnormal transit time, 1 underwent anterior resection, and 2 had a temporary colostomy. In 7 out of 8 children with hypoganglionosis and 9 out of 10 children with a reduced parasympathetic tone the transit time was prolonged. A resection was performed in 7 and 2 of these children respectively. Both patients with heterotopia of the myenteric plexus had a prolonged bowel transit and parts of the large bowel had to be resected. Only 11 out of 17 children with heterotopia of the submucous plexus, dysganglionosis, or immature ganglia had a prolonged transit time, 2 underwent sphincteromyotomy. At follow-up, all patients with malformations other than aganglionosis stated that symptoms had improved and they were willing to tolerate their complaints. However, 25 reported on persistent constipation, 6 on overflow encopresis. All children who required surgery had a prolonged intestinal transit time, but also 21 (56.8%) of 37 children who were successfully treated without surgery. None of the 16 children with normal transit had to be operated. It is concluded that specific histochemical findings do not always correlate with delayed intestinal transport. The determination of the intestinal transit time represents an important tool to identify the clinical relevance of histochemical findings in the individual patient.