The issue of organ protection has always occupied a special position in cardiac surgery due to the use of cardiopulmonary bypass (CPB). CPB is a necessary part of most cardiac surgeries. However, perfusion also poses an advanced risk for the patient’s organs and systems. Brain is very sensitive to various pathological influences. Thus, on-pump surgery often results its damage and disruption of normal function for a short or long period. The authors report such violations and their incidence. In addition, attention is focused on pathophysiological mechanisms of cerebral damage under CPB considering the concept of neurovascular unit of the brain. These factors are cerebrovascular embolism, insufficient cerebral oxygenation, intraoperative transfusion and systemic inflammatory response as a multifactorial process. Etiology of this process includes all of the above-described factors, as well as many others mentioned in the article. The authors discuss the modern methods of monitoring and prevention of these complications.