Objective: Three-dimensional cone-beam computed tomography is gaining popularity as an imaging modality aiding the performance of difficult endodontic treatment procedures. For this reason, we assessed the visualization of bioactive furcal perforation repair materials in an ex vivo study using CBCT with different voxel sizes and determined which voxel size yielding the best images with least artefacts. Visualization of endodontic restorative material is affected by the appearance of various artifacts. This study was conducted to evaluate the CBCT visualization of three perforation repair materials using five different voxel sizes. Methods: This study was performed with 84 mandibular molars that had been extracted for various reasons. All samples were measured with a digital caliper (Digimess, São Paulo, Brazil), marked at 3 mm above the cementoenamel junction, and decoronized at this line. The root segments were amputated at 3 mm below the furcation site using diamond discs under water cooling. The openings of the pulp chamber created, following the furcation defects formed. Biodentine, MTA, and EndoSequence were mixed following the manufacturers’ instructions and applied to the perforation sites. Five image sets were obtained: 75 micron, 100 micron, 150 micron, 200 micron, and 400 micron. 2 examiners were evaluated the images independently. Results: The best image quality for all repair materials obtained in 100 micron. Image clarity of repair materials showed no significant difference among voxel sizes of 75 and 150 micron. Image quality was significantly reduced at 200 and 400 micron voxel sizes, and the worst quality was obtained at 400 micron voxels in all groups. Conclusions: CBCT imaging can be used to examine endodontic repair materials with adjustment of the effective radiation dose rate and selection of the appropriate voxel size.