Cardiac surgery using cardiopulmonary bypass (CPB) provokes a systemic inflammatory response. This is mainly triggered by contact activation of blood by artificial surfaces of the extracorporeal circuit. Although often remaining sub-clinical and resolving promptly at the end of CPB, in its most extreme form this inflammatory response may be associated with the development of the systemic inflammatory response syndrome (SIRS) that can often lead to major organ dysfunction (MODs) and death. Here, we review the pathophysiology behind the development of this “whole body” inflammatory response and some of the methods currently used to minimise it.