Appropriate nephron function is dependent on the detailed spatial interrelationship of blood vesselswith the tubular components. However, because of methodological limitations,the three-dimensional anatomical complexity of the renal vasculatureand its geometrical relationship with specific tubular segmentsalong the nephron has been difficult to study in a quantitativemanner. Three-dimensional microcomputed tomography (3D micro CT) offers the unique opportunity to image kidney sample volumes with a high spatial resolution (of up to 5 µm cubic voxel size) without physically sectioning them, thereby allowing accurate calculations of vessel tortuosity and density, as indices of neovascularization, as well as volume and distribution of various kidney structures. In conjunction with molecular biology techniques, valuable associations between renal microstructures and activation of local molecular pathways can be drawn to elucidate mechanisms of renal disease and design therapeutic approaches. For example, recent studies in animal models of renal hypertension, hypercholesterolemia, and diabetes mellitus have shown that medical intervention to decrease oxidative stress and micro-inflammation may preserve renal microstructures as well as renal function in these chronic renal diseases. Future developments will be needed to establish the place of 3D micro CT in developing, directing, and monitoring the treatment of chronic kidney diseases.