The purpose of this study was to investigate the possible effects of section thickness on volume estimations obtained by cone beam computed tomography. Intraosseal cavities representing bone defects on vestibular sides of the two dry sheep mandibles were scanned by a cone beam computed tomography system. Consecutive sections at 0.2, 0.6, 1, 1.4, and 2.2 mm thickness were used to estimate the volumes of the cavities using the Cavalieri principle of stereological methods. Estimated volumes are then compared with the volumes obtained by the Archimedean principle. In 0.2-, 0.6-, and 1-mm-thick slices, the volumes estimated by the Cavalieri principle did not differ from the volumes by the Archimedean principle (p > 0.05). The 0.2 mm slice-thickness group had the highest asymptotic significance value (p = 0.6). Although the thinnest slice appears to provide the most accurate values, slice thickness up to 1 mm can be chosen for volume calculations on CBCT images.