Cardiopulmonary bypass (CPB) leads to an activation of plasma cascade systems, complement activation, and an acute phase response. To evaluate the influence of the underlying cardiac disease on the activation pattern of these systems, we compared inflammatory changes in coronary artery bypass grafting (CABG) patients with patients undergoing aortic valve replacement. We investigated changes of the acute phase proteins alpha 1-proteinase inhibitor and fibrinogen, the unspecific opsonin fibronectin, and the complement components C3c and C4 induced by extracorporeal circulation in 12 patients undergoing aortic valve replacement and in 12 patients undergoing CABG. Concentrations of C3c and C4 decreased in both groups after the onset of CPB and C4 concentration remained below post-induction levels up to 24 h after onset of CPB (p = 0.04). Fibronectin levels dropped immediately before the onset of CPB (p = 0.01), reaching the lowest values after 20 min of extracorporeal circulation. Fibrinogen and alpha 1-proteinase inhibitor levels after induction of anaesthesia were significantly higher in the CABG group and remained higher throughout the entire study period (p < 0.001). As an indicator of a postoperative acute phase response, concentrations of both proteins rose in the postoperative period above post-induction levels (p < 0.02).