Misalignment of pulmonary vessels (MPV) with alveolar capillary dysplasia (ACD) is a complex congenital vascular abnormality in newborn infants. This condition is often associated with persistent pulmonary hypertension, which leads to severe respiratory distress and finally to the death of the newborn. Here, two cases of MPV with ACD are reported that were associated with atrioventricular septal defects. Both cases showed a combination of a large atrial septal defect and a smaller subvalvular ventricular septal defect. In one newborn, the cardiac malformation was accompanied by a quadricuspid pulmonary valve. These cases emphasize the importance of considering MPV with ACD a possible cause for pulmonary hypertension in the newborn, especially when a concomitant atrioventricular septal defect could represent an alternative explanation for the pulmonary hypertension.