Total colonic aganglionosis occurring together with malrotation is a rare occurrence and may pose diagnostic and management dilemmas for the pediatric surgeon. We report the case of a new born, who was operated at the age of three days for malrotation with volvulus, treated by Ladd procedure. Postoperatively, we noticed persistent abdominal distension and emission of a small amount of meconium every 4 to 5 days. The barium enema showed a non-functional microcolon. Surgical exploration on the 24th day found an ileo-ileal transition zone located 60 cm distal to the ligament of Treitz. Extemporaneous biopsies from the colon and mid-ileum confirmed the absence of ganglion cells. We performed an ileostomy at 50 cm from duodeno-jejunal flexure. Unfortunately, the patient succumbed to nosocomial infection at 33 days of age. This case was a challenging scenario for us where a diagnosis of complicated malrotation had obscured the Hirschsprung’s disease.