Spontaneous aortic thrombosis in the neonate is a rare entity with a high mortality rate. The present patient, who was diagnosed after showing haematuria and cyanosis, underwent aortic thrombectomy with a Fogarty catheter through a left thoracotomy, but died of sepsis, disseminated intravascular coagulation and multiple organ failure. Autopsy revealed multiple residual thrombi in the main branches of the abdominal aorta and necrosis of the abdominal organs despite a patent thoracoabdominal aorta. In patients with no blood flow in the main branches of the abdominal aorta on preoperative examination, removal of thrombi, including those in the main branches of the abdominal aorta, might be performed in a single, early and aggressive procedure.