Nanomaterials are attracting an interest of many researches. All this attention is due the unique physical and chemical properties of nanomaterials differing significantly from the bulk materials mainly due to their size in range of nanometers. Capillary electrophoresis (CE) is a powerful, well-established analytical technique that provides numerous valuable benefits over other separation methods including high-performance liquid chromatography. The connection between CE and nanotechnology can be approached by two strategies: (i) CE analysis of nanomaterials and (ii) nanomaterials for CE improvement. The first perspective focuses on uses of CE as a method for characterization employed during nanomaterial production and modification as well as for monitoring their properties and interactions with other molecules. The second viewpoint deals with applications of nanomaterials for improving CE performance, mainly by enhancing efficiency of separation using nanomaterials as a stationary or pseudo-stationary phase and by enhancing detection sensitivity and/or selectivity in both optical and electrochemical detection. Moreover, applications of nanomaterials for sample preparation before CE analysis will be mentioned. This chapter aims at highlighting the symbiosis of CE and nanotechnology as a combination of modern, progressive field with well-known and reliable analytical method.