Background To examine the influence of voxel sizes to detect of peri-implant fenestration defects on cone beam computed tomography (CBCT) images. Materials and methods This study performed with three sheep heads both maxilla and mandible and two types of dental implant type 1 zirconium implant (Zr 40 ) ( n = 6) and type 2 titanium implant (Ti 22 ) ( n = 10). A total of 14 peri-implant fenestrations (8 buccal surfaces, 6 palatal/lingual surface) were created while 18 surfaces (8 buccal, 10 palatal/lingual) were free of fenestrations. Three observers have evaluated the images of fenestration at each site. Images obtained with 0.75 mm 3 , 0.100 mm 3 , 0.150 mm 3 , 0.200 mm 3 , and 0.400 mm 3 voxel sizes. For intra- and inter-observer agreements for each voxel size, Kappa coefficients were calculated. Results Intra- and inter-observer kappa values were the highest for 0.150 mm 3 , and the lowest in 0.75 mm 3 and 0.400 mm 3 voxel sizes for all types of implants. The highest area under the curve (AUC) values were found higher for the scan mode of 0.150 mm 3 , whereas lower AUC values were found for the voxel size for 0.400 mm 3 . Titanium implants had higher AUC values than zirconium with the statistical significance for all voxel sizes ( p ≤ 0.05). Conclusion A voxel size of 0.150 mm 3 can be used to detect peri-implant fenestration bone defects. CBCT is the most reliable diagnostic tool for peri-implant fenestration bone defects.