Background: Cerebral hypoxia-ischemia remains a complication in children with congenital heart disease. Near-infrared spectroscopy can be utilized at the bedside to detect cerebral hypoxia-ischemia. This study aimed to calibrate and validate an advanced technology near-infrared cerebral oximeter for use in children with congenital heart disease. Methods: After institutional review board approval and parental consent, 100 children less than 12 years and less than 40 kg were enrolled. Phase I (calibration) measured arterial and jugular venous saturation (SaO2, SjO2) by co-oximetry simultaneously with device signals to calibrate an algorithm to determine regional cerebral saturation against a weighted average cerebral saturation (0.7 SjO2 + 0.3 SaO2). Phase II (validation) evaluated regional cerebral saturation from the algorithm against the weighted average cerebral saturation by correlation, bias, precision, and A Root Mean Square assessed by linear regression and Bland-Altman analysis. Results: Of 100 patients, 86 were evaluable consisting of 7 neonates, 44 infants, and 35 children of whom 55% were female, 79% Caucasian, and 41% with cyanotic disease. The SaO2 and regional cerebral saturation ranged from 34% to 100% and 34% to 91%, respectively. There were no significant differences in subject characteristics between phases. For the entire cohort, ARMS, bias, precision, and correlation coefficient were 5.4%, 0.5%, 5.39%, and 0.88, respectively. Age, skin color, and hematocrit did not affect these values. Conclusions: This cerebral oximeter accurately measures the absolute value of cerebral saturation in children over a wide range of oxygenation and subject characteristics, offering advantages in assessment of cerebral hypoxia-ischemia in congenital heart disease. © 2012 The Society of Thoracic Surgeons.