Nanotechnology has significantly impacted on many fields of science, including chemistry, materials, bioanalysis, electronics, optics, medicine and separation science. In separation science, significant advances have been made in electrophoresis and microchip separations employing nanoparticles. Some of the latest advances using nanoparticles include their use as stationary phases for liquid chromatography, gas chromatography, and capillary electrochromatography (CEC), as well as roles as run buffer additives to enhance electrophoresis, and for separation and selectivity control in microchip separations. This review aims to highlight these recent advances.