The role on complement activation of cardiopulmonary bypass (CPB) with its side effects on pulmonary, cardiac and renal function is well known. The biocompatibility of these circulation systems have been improved with heparin-coated circuits. Heparin-coated circuits have dramatic effects on the coagulation cascade, but their role on complement activation has not been clearly defined. in this clinical study the effect of the heparin-coated circuits on complement activation is compared with both consumption of native C3, C4 and also formation of terminal complement complex C5b-9 (TCC). Early postoperative pulmonary function is also determined with measurements of static lung compliance, pulmonary vascular resistance and arterial blood gases. With cardiopulmonary bypass (CPB) native C3 and C4 were consumed, but the differece was not significant between two groups (p>0.05). Also TCC formation increased with CPB, but there were no significant differences between two groups at all measured intervals (p<0.05). Static lung compiance also did not show a significant difference between two groups. Pulmonary vascular resistance was significantly lower in the heparin-coated (HC) group in early postoperative period (p=0.001). We believe that the method of heparin binding may play a role in its diminished effect on complement activation, but tho general augmentation of the circuit’ s biocompatibility may explain its beneficial effect on pulmonary vascular resistance.