Coagulative disorders, especially clotting during extracorporeal membrane oxygenation, are frequent complications. Direct visualization and analysis of deposits in membrane oxygenators using computed tomography (CT) may provide an insight into the underlying mechanisms causing thrombotic events. However, the already established multidetector CT (MDCT) method shows major limitations. Here, we demonstrate the feasibility of applying industrial micro-CT (µCT) to circumvent these restrictions. Three clinically used membrane oxygenators were investigated applying both MDCT and µCT. The scans were analyzed in terms of clot volume and local clot distribution. As validation, the clot volume was also determined from the fluid volume, which could be filled into the respective used oxygenator compared to a new device. In addition, cross-sectional CT images were compared with crosscut oxygenators. Based on the µCT findings, a morphological measure (sphericity) for assessing clot structures in membrane oxygenators is introduced. Furthermore, by comparing MDCT and µCT results, an augmentation of the MDCT method is proposed, which allows for improved clot volume determination in a clinical setting.