A female neonate, born at term, presented with complex cardiac anatomy dominated by right isomerism and infra-diaphragmatic totally anomalous pulmonary venous connection. Surgical repair was performed using circulatory arrest under deep hypothermia. In the postoperative period, the patient could not be weaned off mechanical ventilation, and underwent cardiac catheterization. This revealed major aortopulmonary collateral arteries, which were occluded with coils. We review the literature with specific focus on the occurrence of this unusual combination and its implication in the management during the postoperative period.