This study aimed to evaluate the cause-effect relationship between canal preparation with ProTaper Universal (PTU) system and dentinal defects formation using micro-computed tomography (micro-CT) analysis. Forty mesial canals of mandibular molars with a type II Vertucci's canal configuration were scanned at an isotropic resolution of 14.16 µm. The sample was assigned to an experimental (n = 30) and a control (n = 10) groups, and the mesial canals were prepared with PTU system up to F2 instrument. The specimens from the experimental group were scanned and the cross-section images of the mesial roots, before and after preparation, were screened to identify the presence of dentinal defects. In the control group, the specimens were sectioned perpendicularly to the long axis of the root into 1-mm-thick slices (n = 80) and examined under optical microscope. Once a dentinal defect was detected, the slice was scanned through micro-CT. In the experimental group, dentinal micro-cracks were observed in 4,828 slices (24.04%). In all cross-section images, dentinal defects identified in the postoperative images were already present in the corresponding preoperative image. In the control group, 13 out of 80 slices (16.25%) had at least one dentinal defect visualized under stereomicroscopy, which was identified after a further micro-CT scanning. Micro-CT showed reliability as similar as optical microscopy in detecting dentinal defects, adding the possibility of tracking the dentinal tissue, before and after canal preparation, and providing a clear visualization of micro-cracks. Root canal preparation with PTU system did not induce the formation of new dentinal defects.