The aim of this retrospective study was to compare the morphological features of neurovascular canals and foramina of patients with medication-related osteonecrosis of the jaws (MRONJ) and healthy individuals by using cone beam computed tomography (CBCT). The CBCT images of 58 patients under bisphosphonate therapy diagnosed with MRONJ and age gender- matched controls were retrospectively evaluated. The diameter of mandibular and nasopalatine canal and mandibular, mental and lingual foramina were measured on several sections of CBCT. The value of mental index (MI) and panoramic mandibular index (PMI) were also assessed. The mean value of diametric measurements for all neurovascular canals and foramina in MRONJ patients were narrower than controls. Left mandibular foramen was the most affected area (p<0.001). There were significantly difference in all measurements of mental foramen, lingual foramen and mandibular incisive canal between two groups (p<0.05). PMI of MRONJ subjects were also significantly differences in both sides (p<0.05). In MRONJ patient, neurovascular canals and foramina are affected due to the alterations in bone remodeling. Therefore, the diametric measurement of neurovascular canals and assessment of MI and PMI on CBCT, is a potentially useful method for detection of early changes associated with bisphosphonate therapy and for predict areas where new necrosis may occur.