Many imaging modalities have been described to diagnose and monitor osteoporosis (OP), osteoarthritis and inflammatory rheumatic diseases. Over the last ten years, High Resolution peripheral Quantitative Computerized Tomography (HR-pQCT) was shown to be a precise and non invasive technique to study bone and joint diseases in clinical research. It allows the study of both cortical and trabecular bone microarchitecture at the distal tibia and radius, and further applications have been developed such as the study of mechanical properties by the finite element analysis. Thus, in case-control and cross-sectional studies, microarchitecture parameters discriminated fractured individuals independently of areal BMD. Also, microstructure parameters can predict incident fracture in postmenopausal women. In metabolic diseases associated with bone fragility, HR-pQCT may also be used to explore bone changes. In joint disease studies, HR-pQCT was a remarkable tool to assess bone erosion and joint space narrowing at the hand. This article gives an overview of this imaging technique.