Tissue engineering scaffolds are a promising treatment for bone defects. Micro-CT application for the evaluation of tissue engineering scaffolds for bone surgery and traumatology application is increasing, which comprises in vitro, in vivo and ex vivo studies. Micro-CT itself is not able to replace conventional approaches completely, such as scanning electron microscopy (SEM) or histological examination, but it may offer important benefits regarding non-destructive approach, direct 3D model structure analysis, and visualization and time efficacy. The overview presented herein focuses on a micro-CT application in the field of tissue engineering scaffolds aimed at bone regeneration.