The serum S-100 beta protein level is a specific marker of damage to the central nerve system (CNS). We studied its significance in pediatric cardiac surgery as a possible marker of CNS damage. Subjects were 18 consecutive pediatric patients aged 12 days to 13 years (mean: 2.8 years) undergoing open-heart surgery. We measured the serum S-100 beta protein level using ELISA (SRL Co. Ltd., Tokyo) immediately after inducing anesthesia and immediately, 12 hours, and 24 hours after weaning from cardiopulmonary bypass (CPB). None had postoperative neurological symptoms. The prebypass serum S-100 beta protein level showed a significant logarithmic correlation with patient age. All patients showed increased S-100 beta protein immediately after weaning from CPB, and multiple regression analysis showed that bypass time and cyanosis were significant factors in such as increase. Cyanosis was the only factor in increased S-100 beta protein levels 12 and 24 hours after weaning from CPB. The peak S-100 beta protein level showed a significant exponential correlation with bypass time. Serum S-100 beta protein elevated immediately after weaning from CPB correlated with bypass time but not with neurological symptoms. Physiological changes other than substantial brain damage caused by CPB may increase the serum S-100 beta protein level. Prebypass data on neonates and infants showed serum S-100 beta protein increased without brain damage supporting this hypothesis.