Considering the large number of papers presented in the last years in the field of CE and plate gel electrophoresis (PGE) of nanoparticles and nanoparticle-biomolecule conjugates, this review article gives an overview on the application of capillary electromigration separation techniques for the separation of nanoparticles and nanoparticle-biomolecule conjugates according to differences in size and/or zeta potential and for the determination of several physicochemical parameters characterizing a population of nanoparticles. A brief introduction is given into the theoretical background of the size-selective electrophoretic separation of nanospheres in free-solution and sieving media including involvement of interparticle interactions. Some aspects of colloidal system stability are discussed. Applications of capillary electromigration techniques in the field of size-selective and/or surface charge density-selective separation of nanoparticles and nanoparticle-biomolecule conjugates are described, including free-solution CE, CGE, IEF, and ITP, complemented by an overview on the application of (semipreparative) PGE in the field of nanotechnology and nanobiotechnology. The review also includes actual developments regarding the coupling of capillary electromigration techniques to (wavelength-resolved) LIF and other selective detection methods and studies concerning individual-particle CE.