The strength of bone tissue is not only determined by its mass, but also by other properties usually referred to as bone quality, such as microarchitecture, distribution of bone cells, or microcracks and damage. It has been hypothesized that the bone ultrastructure affects microcrack initiation and propagation. Due to its high resolution, bone assessment by means of synchrotron radiation (SR)-based computed tomography (CT) allows unprecedented three-dimensional (3D) and non-invasive insights into ultrastructural bone phenotypes, such as the canal network and the osteocyte lacunar system. The aims of this study were to describe the initiation and propagation of microcracks and their relation with these ultrastructural phenotypes. To this end, femora from the two genetically distinct inbred mouse strains C3H/He (C3H) and C57BL/6 (B6) were loaded axially under compression, from 0% strain to failure, with 1% strain steps. Between each step, a high-resolution 3D image (700 nm nominal resolution) was acquired at the mid-diaphysis using SR CT for characterization and quantitative analysis of the intracortical porosity, namely the bone canal network, the osteocyte lacunar system and the emerging microcracks. For C3H mice, the canal, lacunar, and microcrack volume densities accounted typically for 1.91%, 2.11%, and 0.27% of the cortical total volume at 2% apparent strain, respectively. Due to its 3D nature, SR CT allowed to visualize and quantify also the volumetric extent of microcracks. At 2% apparent strain, the average microcrack thickness for both mouse strains was 2.0 μm for example. Microcracks initiated at canal and at bone surfaces, whereas osteocyte lacunae provided guidance to the microcracks. Moreover, we observed that microcracks could appear as linear cracks in one plane, but as diffuse cracks in a perpendicular plane. Finally, SR CT images permitted visualization of uncracked ligament bridging, which is thought to be of importance in bone toughening mechanisms. In conclusion, this study showed the power of SR CT for 3D visualization and quantification of the different ultrastructural phases of the intracortical bone porosity. We particularly postulate the necessity of 3D imaging techniques to unravel microcrack initiation and propagation and their effects on bone mechanics. We believe that this new investigation tool will be very useful to further enhance our understanding of bone failure mechanisms.