Purpose To compare two methods of creating three-dimensional representations of mandibular cysts and tumors on the basis of computed tomography (CT) and cone beam computed tomography (CBCT) data. Methods A total of 71 patients with acquired jaw cysts took part in this retrospective clinical study. CT and CBCT scans were obtained from all patients and saved in the Digital Imaging and Communications in Medicine (DICOM) format. Data were analyzed twice with iPlan software. Analysis was performed manually and using an interpolarization algorithm. The accuracy of the two methods in assessing cyst volume was compared. Results Manual delineation did not provide more accurate results than the interpolarization algorithm. Conclusion There are no major differences between manual analysis and analysis using the interpolarization algorithm. The use of the algorithm, however, has the advantage of rapidity.