To describe the different aspects of bone quality, we follow a hierarchical approach and assess bone tissue properties in different regimes of spatial resolution, beginning at the organ level and going down to cellular dimensions. For these purposes we developed different synchrotron radiation (SR) based computed-tomography (CT) methods to assess murine bone ultrastructure. In a first step, a tubular system and the osteocyte lacunar system within murine cortical bone have been established as novel ultrastructural quantitative traits. Results in two mouse strains showed that morphometry of these quantitative traits was dependent on strain and partially on gender, and that their scaling behavior with bone size was fundamentally different. In a second step, we explored bone competence on an ultrastructural level and related our findings to the two ultrastructural quantitative traits introduced before. We showed that SR CT imaging is a powerful tool to investigate the initiation and propagation of microcracks, which may alter bone quality and may lead to increased fracture risk by means of microdamage accumulation. In summary, investigation of ultrastructural bone tissue properties will eventually lead to a better understanding of bone quality and its relative contribution to bone competence.