Bone microstructure has usually been assessed by obtaining samples invasively and analyzing them with conventional histomorphometric methods. Improvements in high-resolution image acquisition systems have enabled non-invasive assessment of bone morphology and a more precise 3-D evaluation by means of "virtual biopsies", permitting bone assessment in regeneration or remodeling processes. This review describes the characteristics and limitations of bone assessment using different high-resolution image systems (synchrotron-radiation computed tomography, micro-computed tomography, acoustic scanning microscope; micro-magnetic resonance imaging). Morphometric variables that can be obtained from these images are reported and compared with conventional histomorphometric variables.