Hirschsprung's disease is an inherited disorder characterized by the absence of ganglion cells in the distal bowel. Neurocutaneous melanosis is a rare congenital syndrome characterized by proliferation of melanin-producing cells in the skin and leptomeninges. The authors described a newborn patient with neurocutaneous melanosis associated with Hirschsprung's disease. This male baby had congenital hydrocephalus, large and multiple pigmented skin nevi, and severe abdominal distension. He showed marked hydrocephalus at birth and underwent a ventriculo-peritoneal shunt at the age of 5 days. Investigations for gut motility disorders revealed typical findings consistent with Hirschsprung's disease involving the rectosigmoid colon. He was surgically treated for Hirschsprung's disease after transanal endorectal pull-through at the age of 7 months. After settlement of the ventriculo-peritoneal shunt, the transanal approach was of significant value for keeping the intraperitoneal catheter clean. The association of developmental disorders of melanocytes and enteric ganglia, both of which originated from the neural crest, suggested the presence of mutual pathogenetic factors in the patient.