We report the case of a newborn with alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV), a rare condition of unknown etiology presenting in the neonatal period with significant persistent pulmonary hypertension. The diagnosis was made by lung biopsy and confirmed at autopsy. Specific genetic analysis demonstrated defects in the FOXF1 gene. The diagnosis of ACD/MPV requires a high level of suspicion and is made by lung biopsy or necropsy examination by a pediatric pathologist with experience in this condition. The availability of genetic testing has led to increasing diagnosis of patients with this lethal disorder and can influence their management, specifically by indicating the need for lung biopsy in a critically ill newborn.