Matrix metalloproteinases (MMPs) and the tissue inhibitors of matrix metalloproteinases (TIMPs) regulate matrix remodeling in the heart. Changes in synthesis and release of MMPs and TIMPs are observed after extracorporeal circulation (ECC). Thus, MMPs and TIMPs are supposed to be involved in ECC-mediated cardiac dysfunction. The aim was to examine the role of MMPs and TIMPs in ECC-mediated cardiac dysfunction. Extracorporeal circulation was instituted in rats for 60 min at a flow rate of 120 ml/kg/min. Three groups (n = 10) were studied: group CAO: 60 min ECC without aortic cross-clamping, group CAC: 60 min ECC including 30 min aortic cross-clamping (crystalloid Inzolen® cardioplegia), and group CAB: 60 min ECC including 30 min aortic cross-clamping (blood cardioplegia). Left ventricular (LV) function was measured with conductance catheter. Matrix metalloproteinase-activity was determined by zymography and TIMP activity was determined by reverse zymography. Gene expression of MMPs and TIMPs was determined by real-time polymerase chain reaction. Sixty minutes after weaning from bypass, there was a preserved LV function in the CAO and CAB group and an impaired LV function in the CAC group. We observed an increased myocardial activity and an increased myocardial messenger RNA expression of MMP-2, MMP-9, TIMP-1, and TIMP-4 in all ECC groups, when compared with sham animals. With regard to enzyme activity, there was an imbalance of MMP/TIMP ratio leading to an increased activity of MMP in the CAC group. In terms of gene expression, there was an imbalance of MMP-2/TIMP-4 ratio leading to an increased expression of MMP-2 in the CAC group. MMP-2 contributes to myocardial reperfusion injury in this in vivo model of ECC with cardioplegic arrest.