Kidneys are a major organ for blood filtration and waste elimination and thus play a key role in the transport and clearance of nanoparticles in vivo. The interactions of nanoparticles with different kidney compartments can be precisely regulated by modulating their size, shape and surface chemistry. The quantitative understanding of nanoparticle–kidney interactions at the molecular level is important for improving disease targeting, precisely controlling nanoparticle transport and clearance, and minimizing the potential health hazards of nanomedicines. In this Review, we summarize the glomerular filtration of macromolecules and nanoparticles in the kidney and survey kidney imaging techniques for the study of nanoparticle–kidney interactions ex vivo and in vivo. We investigate the different transport mechanisms of nanoparticles in the kidneys and discuss size, charge and shape dependencies in renal clearance. Nanoparticles are then investigated for the preclinical and clinical detection and treatment of diseases such as kidney dysfunction and cancer. Finally, challenges and opportunities for renal-clearable nanoparticles are highlighted.