Neonatal spontaneous aortic arch thrombosis without an anatomical correlate is an extremely rare disorder of unknown etiology. A 1-day-old newborn was admitted with suspicion of the coarctation of the aorta. Angiography revealed congenital occluding thrombosis of the ascending aorta and the aortic arch. Surgery was considered impossible because of concomitant thrombosis of the inferior vena cava and the right renal vein. Thrombolysis with streptokinase and tissue plasminogen activator was attempted unsuccessfully. Heterozygous carrier status of the factor V Leiden mutation was diagnosed as a single prothrombotic risk factor. Congenital prothrombotic conditions including factor V Leiden carrier status may serve as risk factors for the development of spontaneous aortic arch thrombosis in neonates. In chronic organized thrombi thrombolytic therapy is likely to fail.