The NanoSIMS ion probe is a new-generation SIMS instrument, characterised by superior spatial resolution, high sensitivity and multi-collection capability. Isotope studies of certain elements can be conducted with 50-100nm resolution, making the NanoSIMS an indispensable tool in many research fields. We review technical aspects of the NanoSIMS ion probe and present examples of applications in cosmochemistry and biological geochemistry. This includes isotope studies of presolar (stardust) grains from primitive meteorites and of extraterrestrial organics, the search for extinct radioactive nuclides in meteoritic materials, the study of lunar samples, as well as applications in environmental microbiology, cell biology, plant and soil science, and biomineralisation.