Deep hypothermic circulatory arrest during repair of aortic arch anomalies may induce neurological complications or myocardial injury. Regional cerebral and myocardial perfusion may eliminate those potential side effects. From March 2000 to March 2002, 48 neonates or infants with complex arch anomaly were operated on using the regional perfusion technique. Thirty-three patients were male and the median age was 24 days (range 5-301 days). Preoperative diagnosis consisted of coarctation or interruption of the aorta associated with ventricular septal defect (group I, n = 26) and arch anomaly with complex intracardiac defects such as hypoplastic left heart syndrome or its variants (group II, n = 22). Arterial cannula was inserted through the innominate artery and the flow rate was regulated to about 50-100 ml/kg per min during regional perfusion. Simultaneous myocardial perfusion was maintained using a Y-connected infusion line. Cardioplegia was applied during intracardiac repair. Cardiopulmonary bypass and aortic cross-clamp times were 154 +/- 49 and 39 +/- 34 min, respectively. Temporary circulatory arrest for intracardiac procedures was performed in eight patients. However, the mean arrest time was minimized (range 1-18 min). The descending aorta clamping time was 33 +/- 16 min. Operative mortality rates in each group were 0 and 18.2% (0/26 and 4/22). Late mortality rates were 0 and 11.1% (0/26 and 2/18) during 9.1 months of follow-up. Complications consisted of low cardiac output in eight cases, transient neurological problems in two cases, and transient renal insufficiency in two cases, respectively. Regional perfusion is feasible and can be used with acceptable results. It may reduce potential complications following aortic arch reconstruction using circulatory arrest. However, repair of aortic arch in the patients with complex intracardiac defects still imposes a significant rate of mortality and morbidity.