Objective: Heparin biocompatible coating frequently is used to reduce inflammation and blood coagulation during cardiopulmonary bypass (CPB) in cardiac surgery. Whether heparin coating is protective or damaging to the vascular endothelium is unclear. The authors investigated whether heparin-coated (HC) circuits are associated with better preservation of microcirculatory perfusion and glycocalyx dimensions compared with nonheparin phosphorylcholine-coated (PC) circuits. Design: Prospective, randomized blinded study. Setting: Tertiary university hospital. Participants: A total of 26 adults undergoing elective coronary artery bypass graft surgery with CPB. Interventions: PC (n = 13) versus HC circuits (n = 13). Measurements and Main Results: Sublingual microcirculatory perfusion was measured before, during, and after CPB using sidestream dark field imaging and analyzed for perfused vessel density and perfused boundary region, an inverse parameter for glycocalyx dimensions. Onset of CPB was associated with an increase in perfused boundary region in the PC group that continued until the third postoperative day (2.0 ± 0.2 to 2.5 ± 0.2 µm; p = 0.018). This was paralleled by increased plasma syndecan-1 levels in the PC group. Contrastingly, both parameters remained unaltered in the HC group compared with baseline levels. CPB decreased perfused vessel density in both groups (CPB v pre-CPB: PC: 17 ± 2 to 13 ± 2 mm/mm2, p = 0.006; HC: 16 ± 2 to 11 ± 2 mm/mm2, p = 0.003) and remained equally altered in the first 3 postoperative days. Conclusion: The use of an HC circuit is associated with better preservation of the endothelial glycocalyx compared with PC circuits, whereas microcirculatory perfusion was disturbed equally in both groups. Hence, CPB-induced microcirculatory perfusion disturbances seem to be coating independent.