Additive manufacturing, and among all stereolithography, has shown great potential in the field of biomedical science. This technology offers a relatively simple means to manufacture objects with complex external and internal features and high spatial resolution, compared to more traditional manufacturing methods. Successful clinical reports of patient specific implants manufactured using 3D printing foster great promises, particularly in the field of craniomaxillofacial reconstruction. However, along with the ability to produce highly defined prostheses, the community still needs tools to ensure the quality of the final products. In this study, we demonstrate that high-resolution micro-computed tomography is an efficient system to control the quality of a 3D-printed structure. As a proof of concept, using stereolithography-printed macroporous scaffolds with various mineral content, we showed that micro-computed tomography allows quantification of shape and morphometry of the specimens; it allows mapping differences between the 3D-printed scaffolds and their original Computer-Aided Design models, and can quantify the influence of the mineral content on the structures. As perspective, the development of micro-computed tomography quality control routines would help ensuring the quality of implants preoperatively, and as such, has the potential to improve surgical outcomes.