Neuronal intestinal dysplasia (NID) of the colon has been reported in adults and children with chronic constipation. However, it is unknown whether these histological abnormalities are related to the severity of symptomatology or the findings of anorectal manometry. We studied 57 children (2 weeks to 17 years old, 33 boys) who had chronic constipation and/or soiling or obstructive symptoms early in life and evaluated anamnestic data, symptoms, outcome after 6 months of conventional therapy, rectal biopsies for signs of dysganglionosis, and results of anorectal manometry. In cooperative patients, defectaion dynamics were recorded during manometry with simultaneous surface electromyogram of the external anal sphincter. In 30 older patients, severity of constipation was assessed by measurement of colonic transit time with radiopaque markers. Histology confirmed Hirschsprung's disease in nine (excluded from further analysis), hyperganglionosis of the plexus submucosus (classic NID) in six, heterotopic ganglion cells without hyperganglionosis (abortive NID) in 18, and no signs of dysganglionosis in 24 patients. The rectoanal inhibitory reflex was more often absent or abnormal in children with classic NID (six of six) and abortive NID (11 of 17) compared with children with normal histology (four of 22) (p < 0.001). All other manometric parameters analyzed, colonic transit times, and clinical outcomes were not related to histological diagnosis. In contrast, the severity of constipation and outcome was significantly worse in children with abnormal defecation dynamics. These results suggest that histological signs of NID in the submucous plexus are of uncertain value in assessing the clinical picture and should not influence decisions concerning further treatment, especially surgical interventions.