Objective To study the therapeutic effects of prostaglandin E1 on the neonates with transposition of the great vessels with intact ventricular septum (TGV/IVS) retrospectively. Method From January 2004 to June 2009, 34 neonates with TGV/IVS were enrolled in this study. The pulse rate and oxygen saturation (SpO2) of patients were measured percutaneouly at admission. Lipo-prostaglandin E1 (Lipo-PGE1) was administered via peripheral vein with pumping infusion continuously after diagnosis by echocardiography in order to keep the ductus arteriosus (DA) patent. The dose and the time required for the Lipo-PGEl to produce effect were recorded. The changes of SpO2 before and after administration of Lipo-PGE1 were observed. The changes of DA's diameter detected by using echocardiography before and during the operation. Results In all patients the initial dose of Lipo-PGEl was 5 ng/( kg·min) except 3 patients whom larger dosed were required to give guided by the change of SpO2 with 10 ng/(kg·min) in two patients and 15 ng/(kg·min) in one patient. The time required for Lipo-PGE to produce the effect was 5-15 minutes in most infants with mean of (12 ± 3) minutes. The mean SpO2 of the patients measured at admission was (80.05±7.64)%, and it was (86.41±4.83)% two hours before operation (P < 0.05). The average diameter of DA was (0.37±0.08) cm at the time diagnosis and it was (0.51 ±0.15) cm during the operation. The adverse effects occurred in two patients and one of them had apnea and was treated mechanical ventilation. Conclusions Lipo-PGE1 given by continuous pumping infusion via peripheral vein in dose of 5 ng per kilogram per minute can maintainthe DA patency and promote the systemic oxygenation and perfusion, improving the circulation and oxygenation and correcting the acidosis until the plastic surgery performed. Most of the adverse effects of PGE1 are dose related.