To describe the case of an infant with Hirschsprung's disease presenting as total colonic aganglionosis, which, after surgical resection of the aganglionic segment persisted with irreversible functional intestinal obstruction; discuss the difficulties in managing this form of congenital aganglionosis and discuss a plausible pathogenetic mechanism for this case. Case description The diagnosis of Hirschsprung's disease presenting as total colonic aganglionosis was established in a two-month-old infant, after an episode of enterocolitis, hypovolemic shock and severe malnutrition. After colonic resection, the patient did not recover intestinal motor function that would allow enteral feeding. Postoperative examination of remnant ileum showed the presence of ganglionic plexus and a reduced number of interstitial cells of Cajal in the proximal bowel segments. At 12 months, the patient remains dependent on total parenteral nutrition. Comments Hirschsprung's disease presenting as total colonic aganglionosis has clinical and surgical characteristics that differentiate it from the classic forms, complicating the diagnosis and the clinical and surgical management. The postoperative course may be associated with permanent morbidity due to intestinal dysmotility. The numerical reduction or alteration of neural connections in the interstitial cells of Cajal may represent a possible physiopathological basis for the condition. © 2016 Sociedade de Pediatria de São Paulo343388392