BACKGROUND Clinical procedures involving extracorporeal blood circulation are potentially complicated by the interaction of various blood systems with foreign surfaces. In cardiopulmonary bypass, exposure of blood to synthetic surfaces generally leads to activation of cellular and humoral blood systems with activation of complement cascade. This reaction can be associated with a variety of postoperation clinical complications such as increased pulmonary capillary permeability, anaphylactic reactions and various degrees of organ failure which contributes to mortality in routine cardiac operations. Application of biocompatible materials in an extracorporeal circuit modifies the normal pattern of blood activation, and therefore potentially may reduce clinical complications in routine cardiac surgery. METHODS To evaluate whether the use of heparin coated extracorporeal circuits could reduce this activation process we performed a study on forty coronary artery bypass graft patients perfused randomly with heparin-coated circuits (Duraflo II, n = 20) or with non-coated circuits (De Bakey roller pump, control n = 20). Standardized heparinization was maintained for both groups of patients during cardiopulmonary bypass. RESULTS The use of heparin-coated circuits resulted in reduction of systemic leukocyte activation of cardiopulmonary bypass reflected by reduced leukocyte and neutrophil counts 24 hours after operation (p < 0.05). Furthermore, blood samples taken from both the right and left atrium after reperfusion revealed that the differences in neutrophil counts between the right and left atrium occur less in the heparin-coated circuit in contrast to the control group (p < 0.05). The pattern of complement activation, probably initiating this inflammatory reaction, was modified by heparin coating in two different aspects. There was a significant reduction of C3 during and after cardiopulmonary bypass in patients perfused with heparin coated circuits as compared with the control group, also there was reduction of C4 after protamine administration in the same groups (p < 0.05). The reductions in blood and complement activation with heparin-coated circuit indicate a substantial improvement in biocompatibility, and consequently reducing clinical complications associated with cardiopulmonary bypass. CONCLUSIONS In conclusions using the Duraflo II heparin-coated circuit in open heart surgery can reduce the complement activation and inflammatory response to cardiopulmonary bypass.