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The aim of this study was to evaluate the accuracy of cone-beam computed tomography (CBCT) for determining cortical thickness and the gray value, investigating its correlation with micro-computed tomography (CT) and histology analysis. Sixty-two bone samples from 4 anatomic regions of the jaw were analyzed. A radiographic surgical stent was used during CBCT and bone sample harvesting. The cortical thickness and gray value of the planned implant were evaluated by CBCT. Bone volumetric fractions, bone mineral density, and % porosity assessed by micro-CT and mineralized material by histology analysis from harvested bone samples were analyzed and assessed for the association with the CBCT using Pearson correlation. A correlation between cortical thickness measured from the CBCT and Micro-CT (r = 0.933, P < 0.01) was identified. There was no difference between gray values measured from the CBCT among regions, while bone density parameters from micro-CT and histologic analysis showed significant difference (P < 0.01) among regions. Bone density parameters from micro-CT and histologic analysis showed correlation with cortical thickness but not with the gray value. In conclusion, CBCT is highly accurate in linear measurements and demonstrated correlation with genuine bone density. However, the gray value could not demonstrate the true bone density according to a low correlation to bone density variable measured from micro-CT and histologic analysis.