A rare case of ileal perforation, as a fatal initial presentation of total colonic aganglionosis (TCA) in infancy is reported. A 10-week-old boy, was brought to the emergency department with symptoms of complicated intestinal obstruction. He looked ill, was lethargic, markedly dehydrated and had a severely distended abdomen. An abdominal X-ray revealed multiple air fluid levels seen in a distended small intestine. During exploratory laparotomy the ileum was massively dilated with distal segment perforation. Ileal perforation repair was performed. A totally collapsed microcolon was identified. Biopsies were taken from the high rectum, sigmoid and hepatic flexure. Appendectomy and ileostomy were performed. All biopsies, as well as the appendix, showed absence of ganglion cells. Despite this procedure the patient progressively deteriorated and later died due to sepsis. Ileal perforation in infants is a rare, but potentially fatal initial presentation of TCA. Early detection is essential to prevent life-threatening complications.