We report a protracted hypoxic event during Soave's endorectal pull-through for Hirschsprung's disease in a 2-month-old male infant with tetralogy of Fallot. After the bowel loops were delivered out of the abdominal cavity, profound hypoxemia occurred which persisted for about 120 min. The hypoxemia was completely resolved after the intestine was reduced back into the peritoneal cavity. The immediate cause was postulated to have been decreased systemic vascular resistance. Associated factors included hypothermia and acidosis leading to high pulmonary vascular resistance which further aggravated the right-to-left blood-shunting situation in this patient. Postoperative follow-up showed no neurological complications. Small infants with complex heart disease should be carefully evaluated before major abdominal surgery.