The purpose of this study was to evaluate the relationship between third molars and the inferior alveolar canal using panoramic radiographs and cone beam computed tomography (CBCT) scans and to assess clinical outcomes after third molar removal retrospectively. The degree of superimposition, buccolingual position (buccal, central, and lingual) and physical relationship (separation, contact, and involved) were measured using CBCT scanning. Post-extraction complications were recorded. Based on radiographic evaluation, 45.9% of third molar roots were inside the inferior alveolar canal, 21.3% were in contact with the inferior alveolar canal, and 32.8% were separated from the canal. The frequency at which the mandibular canal was separated from the root apex was significantly higher when the canal was in the buccal position (80.0%) than in the central (20.0%) and lingual positions (0.0%). Although on panoramic radiographs all third molars were directly superimposed on the inferior alveolar canal, CBCT showed direct contact or canal involvement in 67.2% and separation of the canal from the root apex in 32.8%. Complications occurred in nine patients: eight had third molar root apices inside or in contact with the inferior alveolar canal. The prevalence of post-extraction complications correlated with the absence of cortication around the inferior alveolar canal.