A newborn infant patient presented with persistent pulmonary hypertension. For right ventricular decompression, the ductus arteriosus was kept open by prostaglandin E1 infusion and was stented at the age of 4 weeks during heart catheterization. The child was weaned from mechanical ventilation, since pulmonary functions were adequate. A small atrial septal defect was identified and closed in cardiac catheterization laboratory to decrease preductal hypoxemia. Diagnostic workup led to the diagnosis of alveolar capillary dysplasia with misalignment of the pulmonary veins. Suprasystemic pulmonary arterial hypertension with persisting nitric oxide dependency remained the leading symptoms. The child underwent bilateral lung transplantation at the age of 28 months. He is well at the age of 44 months.