Oxygenator thrombosis is a serious complication in extracorporeal membrane oxygenation (ECMO) and may necessitate a system exchange. Coagulation and fibrinolysis parameters, flow dynamics, and gas transfer performance are currently used to evaluate the degree of oxygenator thrombosis, but there is no technical approach for direct visualization and quantification of thrombotic deposits within the membrane oxygenator (MO). We used multidetector computed tomography (MDCT) with three-dimensional postprocessing to assess the incidence of oxygenator thrombosis, to quantify thrombus extent, and to localize clot distribution. Twenty heparin-coated MOs after successful weaning were analyzed. Mean ECMO support time was 7 ± 4 days, mean activated partial thromboplastin time (aPTT) during ECMO was 59 ± 20 seconds. Thrombotic deposits were detected in all MOs. The mean clot volume was 51.7 ± 22.3 cm. All thrombotic deposits were located in the venous, i.e., inlet part of the device, without apparent evidence of embolization in patients. There was no correlation between clot volume and ECMO support time or aPTT. Clot formation within the MO is a common finding in ECMO despite adequate systemic anticoagulation. The clinical significance of thrombus formation and its influence on gas exchange capacity and hemostatic complications have to be addressed in further studies.