Although closure of an atrial septal defect (ASD II) with an occluding device in the first year of life is not a routine procedure, it is a feasible treatment, even in neonates. Case reports on the off-label use of Amplatzer devices have been repeatedly published, but there are no reports on using the Amplatzer Duct Occluder (ADO) to close an atrial septal defect in a neonate. We report on a successful catheter closure of an ASD II with ADO in a severely cyanotic neonate, seven days after surgical repair of common arterial trunk. Due to progressive cyanosis and clinical signs of right ventricular failure, which developed after common arterial trunk repair, the neonate underwent cardiac catheterization. Diastolic filling impairment of the right ventricle (right ventricle hypertrophy, pulmonary regurgitation, and residual right ventricle outflow tract obstruction) was thought to be the cause of impaired right ventricle diastolic filling, resulting in the right-to-left shunt at the atrial level. Under transesophageal echocardiographic guidance, ADO was delivered through a 5 French sheath into the atrial septal defect. Amplatzer duct occluder closed the defect and proved to be stable in position after disconnection. During the procedure, the child was stable and then transferred to the intensive care unit with significantly improved oxygen saturation. This is the first report on placing a duct occluder in the atrial septal position, which is a novel procedure for-small neonates.