Many bones within the axial and appendicular skeleton are subjected to repetitive, cyclic loading during the course of ordinary daily activities. If this repetitive loading is of sufficient magnitude or duration, fatigue failure of the bone tissue may result. In clinical orthopedics, trabecular fatigue fractures are observed as compressive stress fractures in the proximal femur, vertebrae, calcaneus and tibia, and are often preceded by buckling and bending of microstructural elements. However, the relative importance of bone density and architecture in the aetiology of these fractures is poorly understood. The aim of the study was to investigate failure mechanisms of 3D trabecular bone using micro-computed tomography (mCT). Because of its nondestructive nature, mCT represents an ideal approach for performing not only static measurements of bone architecture but also dynamic measurements of failure initiation and propagation as well as damage accumulation. For the purpose of the study, a novel micro-compression device was devised to measure loaded trabecular bone specimens directly in a micro-tomographic system. A 3D snapshot of the structure under load was taken for each load step in the mCT providing 34 mm nominal resolution. An integrated mini-button load cell in the compression device combined with the displacement computed directly from the mCT scout view was used to record the load-displacement curve. From the series of 3D images, failure of the trabecular architecture could be observed, and in a rod-like type of architecture it could be described by an initial buckling and bending of structural elements followed by a collapse of the overloaded trabeculae. A computational method was developed to quantify individual trabecular strains during failure. The four main steps of the algorithm were (i) sequential image alignment, (ii) identification of landmarks (trabecular nodes), (iii) determine nodal connectivity, and (iv) to compute the nodal displacements and local strains. It was found that for a 1% global strain, the localized strains between nodes were as high as eight times and six times the global compressive and tensile strains, respectively. This provided further evidence for a band-like, local failure of trabecular bone. In conclusion, micro-compression in combination with 3D mCT allows visualization and quantification of failure initiation and propagation and monitoring of damage accumulation in a nondestructive way. We expect these findings to improve our understanding of the relative importance of density, architecture and load in the aetiology of spontaneous fractures of the hip and the spine. Eventually, this improved understanding may lead to more successful approaches to the prevention of age-related fractures.