3D analysis of animal or human whole teeth and alveolar bone can be performed with high sensitivity in a nondestructive manner by microcomputed tomography. Here we describe the protocols to be followed for the most common applications in the developmental studies of dental and craniofacial tissues. Emphasis is placed on the basis of choosing settings for image acquisition, such as voxel resolution (Fig. 1), or beam energy (Fig. 2) and for processing, such as segmentation method (Fig. 3), parameters. The limitations to take into account for optimal efficiency and image quality are also explained.