Cone-beam computed tomography (CBCT) is a new technology in the field of intraoral imaging which allows 3D visualization of the areas scanned. The aim of our study was to assess the capabilities of CBCT in assessment of dental status, crown and root morphology, dental pathologies, tooth wear and enamel hypoplasia in a sample of 117 teeth from Mesolithic (9000 - 6400 calBC) and Neolithic (6200 - 5300 calBC) individuals from the Central Balkans. The study was carried by CBCT imaging of one root teeth placed in wax rim and stone cast to obtain digital images and 3D reconstructions for odontological assessment. All of the 117 teeth examined showed morphological similarity, similar color, shape, mesio-distal ratio and the presence of significant tooth wear. A few specimens displayed signs of radicular and apical pathology and infractions. In 17 teeth the presence of multiple root canals has been confirmed. Enamel hypoplastic defects were clearly observed and accurate measurements performed in order to evaluate the severity of hypoplasia. The use of CBCT supports the information obtained from archeological, anthropological and DNA investigations. It would seem that there is potential for significant development to be made in the research of paleodontological material using non invasive techniques such as CBCT that could play a crucial role in the investigation of bioarchaeological remains.