Thrombotic events are very unusual in neonatal period. This congenital anomaly may be caused by certain risk factors such as polycythemia, perinatal asphyxia, septicemia, maternal diabetes, dehydration, and low cardiac output, or it may occur upon catheterization of central lines. A 20-day-old neonate was referred to our ward with primary signs of hypertrophic cardiomyopathy (HCMP). Echocardiography and CT-angiography were performed to find stenosis or no stenosis of aortic valve, which showed a great mass into the ascending aorta. This mass was resected and removed successfully and thereafter the aortic arch was repaired. There was no prothrombic disorder in his family history.