Surgical treatment of complex congenital heart disease under extracorporeal circulation is accompanied by a systemic inflammatory reaction occurring in neonatal infants and babies. There were drastic increases in the concentration of tumor necrosis factor, interleukin-8, neutrophilic elastase and a predominance of a proinflammatory response over an inflammatory one at the warming stages and after administration of protamine sulfate. The rate of an inflammatory response depended on the duration of extracorporeal circulation. Modified ultrafiltration could remove cytokines; however, their concentration in the body remains high. A relationship was found between the course of a postoperative period and the rate of a developing reaction to extracorporeal circulation in the surgical treatment of congenital heart diseases.