Objective: To quantify tooth volume differences from extracted teeth when using three different three-dimensional (3D) computed tomography (CT)-based imaging modalities. Design: Ex vivo study. Setting: Laboratory and clinics of the University of Alberta. Methods: Cone-beam CT (CBCT) of 12 extracted teeth were scanned using 0.25- and 0.30-mm voxel size from CBCT and a 0.06-mm voxel size from micro-CT (reference standard). 3D reconstructions for each tooth from each imaging modality were made through the software ITK-SNAP®. The mean volume differences between each pair of scanning modalities were calculated and then compared and analysed through a repeated measures ANOVA. Results: The average overestimations of the teeth volume were 15.2% for the high-resolution CBCT and 28.1% for the low-resolution CBCT compared to micro-CT measurements. The differences in absolute volume were 81.6 mm3 and 152.8 mm3, respectively. All differences were statistically significant ( P < 0.05). Conclusions: Orthodontists and researchers who assess root resorption through CBCT imaging should be aware that the depicted volumes may likely be overestimating tooth volume and camouflaging real root volumetric treatment changes.