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Objectives: This study aimed to compare the diagnostic accuracy of cone beam CT (CBCT) units with different voxel sizes with the digital intraoral scanning technique in terms of the detection of periodontal defects. Methods and materials: The study material comprised of 12 dry skulls with maxilla and mandible. Artificial defects were created on teeth separately using burs randomly on dry skulls. In total 46 dehiscences, 10 fenestrations, 17 furcations, 12 wall defects and 13 without periodontal defect were used in the study. Each tooth with and without defects was imaged at various vertical angles using each of the following modalities: a Veraviewepocs 3D R100 CBCT device and a 3D Shape TRIOSㄾ Color P13 Shade Intraoral Scanner. Results: The κ values for interobserver agreement between observers ranged between 0.29 and 0.86 for the CBCT 10 × 8 cm field of view (FOV) with 0,160 mm3 voxel size; 0.35 and 1 for the CBCT 8 × 8 cm FOV with 0,125 mm3 voxel size; and 0.30 and 1 of intraoral scans. The κ values for detecting defects on anterior teeth were the least, following premolar and molar teeth both CBCT and intraoral scanning. Conclusions: Smaller voxel sizes and smaller CBCT FOV has the highest sensitivity and diagnostic accuracy for detecting various periodontal defects among the scanner modalities examined. Advances in knowledge: Adequate evaluation of the condition of the alveolar bone and periodontal tissues is important for the diagnosis, treatment, and prognosis of periodontal disease. Limited examination methods, such as palpation, inspection, and periodontal probe examination, may provide insufficient information for the diagnosis of periodontal diseases.