Cerebral fractional oxygen extraction (FOE) was monitored in 30 children, using near infrared spectroscopy during cardiopulmonary bypass, to investigate the effect of hypothermia and circulatory arrest. One group of children (n = 15) underwent profound hypothermia with total circulatory arrest (n = 8) or continuous flow (n = 7). Another group (n = 15), of whom only one had circulatory arrest, underwent mild (n = 6) or moderate (n = 9) hypothermia. The mean FOE (SD) before bypass was 0.35 (0.12) and this correlated negatively with the preoperative arterial oxygen content (r = -0.58). Between the stage of cooling on bypass and cold bypass there was a reduction in FOE in all groups. Between cold bypass and rewarming there was an increase in FOE only in the groups with continuous flow. In the circulatory arrest group, the FOE remained low during rewarming and was significantly lower than that of the continuous flow group. No patients died and none had neurological abnormalities postoperatively. Apparent changes in oxidised cytochrome oxidase concentration were also monitored using near infrared spectroscopy. There was a fall in cytochrome aa3 on starting cardiopulmonary bypass, but there were no significant differences in the changes in cytochrome aa3 between any stage in any of the patient groups. Using this non-invasive technique, cooling was shown to reduce cerebral FOE. During rewarming on bypass there was an increase in cerebral FOE only in patients who had had continuous flow bypass. In contrast, the cerebral FOE in those with circulatory arrest remained constant after arrest and during the duration of the study. This may have implications for the timing of hypoxic brain injury.