Premature closure of the foramen ovale (FO) is a rare congenital anomaly that results in a wide spectrum of hemodynamic findings. We experienced the case of a male neonate with this condition who, at birth, showed unique hemodynamics that was similar to that in hypoplastic left heart syndrome, despite having a normal sized left ventricle (LV). His systemic blood flow was dependent on patent ductus arteriosus (DA). Echocardiography on day 0 revealed retrograde flow in the ascending aorta. We could not detect flow across the interatrial septum, and diagnosed premature closure of FO. Because his LV was not hypoplastic, we considered that the systemic blood flow would be maintained by LV output after lung circulation was established. We infused prostaglandin E1 incorporated in lipid microspheres (lipo-PGE 1 ), which confirmed the retrograde flow in the ascending aorta. We stopped the lipo-PGE 1 infusion after the flow in the ascending aorta became antegrade on day 2. After DA closed, systemic blood flow was maintained by LV output, and normal circulation was established. In addition to the congenital heart anomaly, several other anomalies were noted, including a downslanting of the palpebral fissure, micrognathia, and cryptorchidism. A cytogenetic analysis revealed der(20)t(6;20) (q25.2;p13), and 6q duplication syndrome was diagnosed. The patient was discharged without any medications on day 54 despite the presence of mild pulmonary hypertension. This is probably the first report of premature closure of FO in a patient with such hemodynamics and the first one of premature closure of FO associated with 6q duplication syndrome.