BACKGROUND: Appropriate placement of aortic and venous cannulas is important to ensure effective systemic perfusion. The malposition of the aortic cannula may promote preferential flow down the aorta or induce flow to aortic arch vessels causing pressure gradient between mean radial arterial pressure (RAP) and femoral arterial pressure (FAP). In this study we compared mean radial to femoral artery pressure gradient before and immediately after aortic cannulation and during cardiopulmonary bypass (CPB). METHODS: Ninety two pediatric patients undergoing open heart surgery were examined. After induction of anesthesia RAP and FAP were measured. The pressure gradient was measured before and after aortic cannulation, 15, 30 and 60 minutes after aortic cross clamping (ACC). When the pressure gradient of more than 10 mmHg developed, the surgeon was recommended to manipulate position of the aortic cannula. If the pressure gradient returned to pre-CPB level after manipulation, the pressure gradient was considered to develop due to aortic cannula. The age, presence of cyanosis, adjustment of shape of aortic cannula tip before cannulation and side of radial artery cannulation as factors developing pressure gradient were examined. RESULTS: Fifteen patients (16.3%) developed pressure gradient due to position of aortic cannula. Two patients (2.2%) developed immediately after aortic cannulation and fourteen patients (15.2%) during CPB. There was no statistically significant factor developing pressure gradient except non-cyanotic disease. CONCLUSIONS: The pediatric patient could develop pressure gradient due to malposition of aortic cannula frequently during CPB. Therefore, the simultaneous monitoring of RAP and FAP may be beneficial for managing CPB in pediatric cardiac surgery.