Neuropsychological and neurological deficits are still major causes of mortality and morbidity after cardiac operations and are thought to be caused by embolism and cerebral hypoxia. Near-infrared spectrophotometry (NIRS) is a promising method for non-invasive monitoring of cerebral oxygenation and hemodynamics. Different devices provide information on changes of oxygenated (HbO2) and deoxygenated hemoglobin (Hb), oxidized cytochrome aa3 (CytOx) or regional oxygen saturation (rSO2). NIRS has been applied to patients during adult and pediatric cardiovascular surgery with and without deep hypothermic circulatory arrest (DHCA). In most of the studies, significant changes in cerebral oxygenation were detected by NIRS. NIRS measurements were influenced by the cerebral oxygen metabolism and the operative management. However, clinical, experimental, and theoretical issues raise doubts as to the clinical relevance of the hemoglobin saturation (HbO2, Hb, rSO2 signals) during hypothermia and alkalosis, because the oxygen affinity of hemoglobin increases and a high saturation might simply reflect the inadequate oxygen transport into cells. In contrast, recent experiments have proved a high correlation between the CytOx signal and the MRS parameters nucleoside triphosphate and phosphocreatine. Histological damage was significantly related to the lowest CytOx value; in a clinical study it predicted impaired neuropsychological outcome. Therefore, the CytOx signal is of great interest for future studies. NIRS must prove its ability to diagnose cerebral hypoxia consistently during cardiac surgery in a large patient study before this method is brought into routine clinical practice. Absolute quantification and definitions of critical oxygenation margins will be helpful for this goal.