Cyanosis in a newborn is commonly due to intracardiac shunts or duct-dependent lesions. Systemic venous anomalies are uncommon and sinus venous atrial septal defects do not usually present with cyanosis. We report the case of a 4-month-old female with persistent hypoxemia due to a right superior vena cava overriding a superior sinus venous atrial septal defect resulting in a right to left shunt.