The purpose of this analysis was critically to examine the changes of cerebral cytochrome oxidase as detected by near-infrared spectrophotometry (NIRS) during induction of cardiopulmonary bypass (CPB) in fourteen children undergoing open heart surgery. Five children were hypoxaemic (arterial oxygen saturation 49%-84%) before the switch to CPB and nine children were not. In the hypoxaemic children, the total cerebral hemoglobin concentration [tHb] decreased rapidly and markedly, reaching a plateau after 2 min. Surprisingly, cytochrome aa3 concentration in its oxygenated form [CytO2] decreased in parallel while the cerebral haemoglobin oxygenation index [HbO2]-[Hb] increased gradually. In the eight normoxaemic children, changes in the NIRS signals were insignificant. When a standard NIRS algorithm was used, the magnitude of the change in [CytO2] was closely associated with the magnitude of the change in [tHb] (p < 0.0001), the time courses of the [CytO2] and [tHb] signals were parallel in 11 of the 14 children and the error of fit in the NIRS multicomponent analysis increased 10- to 100-fold over system noise. A new NIRS algorithm, using wavelength specific optical pathlengths, did not improve the error of fit but produced smaller estimates of [CytO2] changes, which were unrelated to the [tHb] changes. In our opinion the interesting possibility of monitoring cytochrome oxidation by NIRS requires further validation.