We describe a non-destructive imaging method, named contrast-enhanced nanofocus X-ray computed tomography (CE-nanoCT), that permits simultaneously imaging and quantifying in 3D the (sub)tissue architecture and (biochemical) composition of cartilage and bone in small animal models at a novel contrast and spatial resolution. To demonstrate the potential of this novel methodology, a newborn mouse was scanned using CE-nanoCT. This allowed simultaneously visualising the bone and cartilage structure much like the traditional alcian blue-alizarin red skeletal stain. Additionally, it enabled a 3D visualisation at such a high spatial image resolution that internal, micro-scale structures could be digitally dissected and evaluated for size, structure and composition. Ex vivo treatment with papain, that is known to specifically remove the non-calcified cartilage layer but keep the calcified cartilage intact, proved CE-nanoCT to be applicable to visualise the subdivisions within the hyaline cartilage of the articular joint of mice. The quantitative power of CE-nanoCT in vivo was evaluated using a mouse model for osteoarthritis (OA), where OA-like cartilage lesions are induced by meniscus destabilisation surgery. The thickness of both the non-calcified and calcified cartilage layer in the knee joint of such mice was visualised and quantified in 3D and compared to unaffected mice. Finally, to show that different forms of cartilage and tissue combinations can be distinguished using CE-nanoCT, different cartilaginous body parts of the mouse were imaged. In conclusion, CE-nanoCT can provide novel insights in preclinical research by quantifying in a non-destructive 3D manner pathological differences, in particular in developing mice, newborns or adults.