The aim of this investigation was to analyze the impact of intermittent cold blood cardioplegia (ICC) and intermittent warm blood cardioplegia (IWC) on endothelial injury in patients referred to elective on-pump coronary artery bypass graft (CABG) surgery. Patients undergoing CABG procedures were randomized to either ICC or IWC. Myocardial injury was assessed by CK-MB and cardiac troponin T (cTnT). Endothelial injury was quantified by circulating endothelial cells (CECs), von Willebrand factor (vWF), and soluble thrombomodulin (sTM). Perioperative myocardial injury (PMI) and major adverse cardiac events (MACE) were recorded. Demographic data and preoperative risk profile of included patients (ICC: n = 32, IWC: n = 36) were comparable. No deaths, PMI, or MACE were observed. Levels of CK-MB and cTnT did not show intergroup differences. Concentrations of CECs peaked at 6 h postoperatively with significantly higher values for IWC-patients at 1 h (ICC: 10.1 ± 3.9/mL; IWC: 18.4 ± 4.1/mL; P = 0.012) and 6 h (ICC: 19.3 ± 6.2/mL; IWC: 29.2 ± 6.7/mL; P < 0.001). Concentrations of vWF (ICC: 178.4 ± 73.2 U/dL; IWC: 258.2 ± 89.7 U/dL; P < 0.001) and sTM (ICC: 3.2 ± 2.1 ng/mL; IWC: 5.2 ± 2.4 ng/mL; P = 0.011) were significantly elevated in IWC-group at 1 h postoperatively. This study shows that the use of IWC is associated with a higher extent of endothelial injury compared to ICC without differences in clinical endpoints.