Bone’s biomechanical properties derive from the hierarchical arrangement of its constituents with toughening mechanisms acting at every length scale. At the nanoscale, bone is a natural composite material consisting of protein (90% collagen and 10% non-collagenous proteins), mineral, and water. These components, their complex arrangement, interactions between them, and organisation of the mineralised collagen fibrils, make bone a tough and strong composite. However, almost nothing is known about how these components contribute to bone’s toughness at the microscale. In this thesis, the elastic and fracture properties of collections of mineralised collagen fibrils bone were assessed at the micrometre scale by developing an in situ scanning electron microscope that minimizes the effects of porosity and heterogeneities. We assessed elastic moduli and fracture toughness by uniaxial micro-compression and double cantilever beam micromechanical approaches, respectively. Microscopic samples of mouse bone femorae were micromachined using a focused ion beam both parallel (longitudinal orientation) and perpendicular (transverse orientation) to the principle bone growth direction. Subsequent transmission electron microscopy imaging of regions of the fractured pillars were used to correlate the role of the local organization of the mineralized collagen fibrils with fracture toughness and crack path. Finally, an experimental protocol was optimised to test the in situ mechanical properties of hydrated healthy tissue. By probing healthy dry samples, we demonstrate that fibril anisotropy plays a pivotal role in the micromechanical response of healthy bone samples and that the crack propagation path in the healthy bone samples relates to local fibrillar orientation. Additionally, osteopontin-deficient bone was studied to elucidate the structure-function relationships in pathological bone associated with deficiencies in non- collagenous proteins. In the osteopontin-deficient bone, the mineralised collagen was less organised localised and deviations in the fibrillar organisation reduced anisotropy, which results in mechanical deterioration of bone (elasticity and fracture resistance) at the microscale.