Objectives: To compare microarchitecture parameters of bone samples scanned using micro-CT (mCT) to those obtained by using CBCT. Methods: A bone biopsy trephine bur (3 3 10 mm) was used to remove 20 cylindrical bone samples from 20 dry hemimandibles. Samples were scanned using mCT (mCT 35; SCANCO Medical, Brüttisellen, Switzerland) with a voxel size of 20 mm and CBCT (3D Accuitomo 170; J. Morita, Kyoto, Japan) with a voxel size of 80 mm. All corresponding sample scans were aligned and cropped. Image analysis was carried out using BoneJ, including the following parameters: skeleton analysis, bone surface per total volume (BS/TV), bone volume per total volume (BV/TV), connectivity density, anisotropy, trabecular thickness and spacing, structure model index, plateness and fractal dimension. Pearson and Spearman correlation coefficients (R) were calculated. CBCT values were then calibrated using the slope of the linear fit with the mCT values. The mean error after calibration was calculated and normalized to the standard deviation of the mCT values. Results: R-values ranged between 0.05 (plateness) and 0.83 (BS/TV). Correlation was significant for both Spearman and Pearson's R for 8 out of 16 parameters. After calibration, the smallest normalized error was found for BV/TV (0.48). For other parameters, the error range was 0.58-2.10. Conclusions: Despite the overall correlation, this study demonstrates the uncertainty associated with using bone microarchitecture parameters on CBCT images. Although clinically relevant parameter ranges are not available, the errors found in this study may be too high for some parameters to be considered for clinical application.