Pulmonary arterial endarteritis is a rare event even in patients with congenital heart disease. In this paper, the authors report two cases of pulmonary endarteritis diagnosed at autopsy. The first was a 3-month-old male infant with absence of congenital heart defect (who had had neonatal sepsis). This patient presented with pneumonia and succumbed within 36 hours of hospital stay despite appropriate antimicrobial therapy and supportive management. The second patient was a 13-month-old male child with previously undiagnosed tetralogy of Fallot who had clinical presentation of acute meningitis with convulsions and succumbed within 12 hours of hospital stay despite adequate treatment. The main autopsy findings were chronic arteritis of the pulmonary trunk and right pulmonary artery in the former and rupture of the pulmonary trunk in the latter.