Background Suboptimal tissue perfusion and oxygenation may be the root cause of certain perioperative complications in neonates and infants having complicated aortic coarctation repair. Practical, effective, and real-time monitoring of organ perfusion and/or tissue oxygenation may provide early warning of end-organ mal-perfusion. Methods Neonates/infants who were scheduled for aortic coarctation repair with cardiopulmonary bypass (CPB) and selective cerebral perfusion (SCP) from January 2015 to February 2017 in Children's Hospital of Nanjing Medical University participated in this prospective observational study. Cerebral and somatic tissue oxygen saturation (SctO(2) and SstO(2)) were monitored on the forehead and at the thoracolumbar paraspinal region, respectively. SctO(2) and SstO(2) were recorded at different time points (baseline, skin incision, CPB start, SCP start, SCP end, aortic opening, CPB end, and surgery end). SctO(2) and SstO(2) were correlated with mean arterial pressure (MAP) and partial pressure of arterial blood carbon dioxide (PaCO2). Results Data of 21 patients were analyzed (age=75 +/- 67 days, body weight=4.4 +/- 1.0 kg). SstO(2) was significantly lower than SctO(2) before aortic opening and significantly higher than SctO(2) after aortic opening. SstO(2) correlated with leg MAP when the measurements during SCP were (r=0.67, p<0.0001) and were not included (r=0.46, p<0.0001); in contrast, SctO(2) correlated with arm MAP only when the measurements during SCP were excluded (r=0.14, p=0.08 vs. r=0.66, p<0.0001). SCP also confounded SctO(2)/SstO(2)'s correlation with PaCO2; when the measurements during SCP were excluded, SctO(2) positively correlated with PaCO2 (r=0.65, p<0.0001), while SstO(2) negatively correlated with PaCO2 (r=-0.53, p<0.0001). Conclusions SctO(2) and SstO(2) have distinct patterns of changes before and after aortic opening during neonate/infant aortic coarctation repair. SctO(2)/SstO(2)'s correlations with MAP and PaCO2 are confounded by SCP. The outcome impact of combined SctO(2)/SstO(2) monitoring remains to be studied.