Neonatal arterial thrombosis is a very rare entity with clinical findings resembling coarctation of aorta or interrupted aortic arch. A two day-old male newborn was admitted to a different hospital with difficulty in sucking and sleepiness. On echocardiographic examination, a diagnosis of interrupted aortic arch was made and he was treated with prostoglandin E2. When the patient presented to our center, physical examination revealed that his feet were bilaterally cold. The pulses were not palpable and there were ecchymotic regions in the lower extremities. Echocardiography ruled out interrupted aortic arch. Computerized tomographic angiography revealed a large thrombosis and total occlusion of the abdominal aorta. Since there was no response to treatment with tissue plasminogen activator, we performed thrombectomy. Homozygous Factor V Leiden and Methylenetetrahydrofolate reductase mutations were found in this patient. Neonatal aortic thrombosis which is observed very rarely and fatal should be considered in the differential diagnosis of coarctation of aorta and interrupted aortic arch. (Turk Pediatri Ars 2015; 50: 118-22)