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Objective: Cone-beam computed tomography (CBCT) has been proposed in surgical planning of lower third molar extraction. The aim of the present study was to assess the reliability of CBCT in defining third molar root morphology and its spatial relationships with the inferior alveolar nerve (IAN). Materials and Methods: Intraoperative and radiographic variables of 74 lower third molars were retrospectively analyzed. Intraoperative variables included IAN exposure, number of roots, root morphology of extracted third molars, and presence/absence of IAN impression on the root surface. Radiographic variables included presence/absence of the cortex separating IAN from the third molar roots on CBCT examination, number of roots and root morphology on both orthopantomography (OPG) and CBCT. The statistical association between variables was evaluated using the Fisher's exact test. Results: In all cases of intraoperative IAN exposure, the cortex appeared discontinuous on CBCT images. All cases, in which the cortical bone was continuous on CBCT images, showed no association with nerve exposure. In all cases in which nerve impression was identified on the root surface, the IAN cortex showed interruptions on CBCT images. No nerve impression was identified in any of the cases, in which the cortex appeared continuous on CBCT images. CBCT also highlighted accessory roots and apical anomalies/curvatures, not visible on the OPG. Conclusions: CBCT seems to provide reliable and accurate information about the third molar root morphology and its relationship with the IAN.