Micro computed tomography (µCT) follows the same principle of computed-tomography used for patients, however providing higher-resolution. Using a non-destructive approach, samples can be scanned, and each section obtained is used to build a volume using tridimensional reconstruction. For bone analysis, it is possible to obtain information about the tissue's microarchitecture and composition. According to the characteristics of the bone sample (e.g. human or animal origin, long or irregular shape, epiphysis or diaphysis region) the pre-scanning parameters must be defined. The resolution (i.e. voxel size) should be chosen taking into account the features that will be evaluated, and the necessity to identify inner structures (e.g. bone channels and osteocyte lacunae). The region of interest should be delimited, and the threshold that defines the bone tissue set in order to proceed with binarization to separate the voxels representing bone from the other structures (channels, resorption areas, and medullary space). Cancellous bone is evaluated by means of the trabeculae characteristics and their connectivity. The cortex is evaluated in relation to the thickness and porosity. Bone mineral density can also be measured, by the amount of hydroxyapatite. Other parameters such as structure-model-index, anisotropy, and fractal dimension can be assessed. In conclusion, intrinsic and extrinsic determinants of bone quality can be assessed by µCT. In dentistry, this method can be used for evaluating bone loss, alterations in bone metabolism, or the effects of using drugs that impair bone remodeling, and also to assess the success rate of bone repair or surgical procedures.