The possibilities and applications of capillary electrophoresis (CE) as an analytical technique for plant secondary metabolites are reviewed. Applications of both capillary zone electrophoresis and micellar electrokinetic capillary chromatography for this purpose are described. CE is compared with high pressure liquid chromato‐graphy (HPLC) as an analytical technique, and the advantages and criticisms of CE are described. The effects of the applied voltage, capillary temperature, electrolyte concentration and nature (complexing or non‐complexing buffers), buffer pH, micelle concentration and nature (sodium dodecyl sulphate or cetyltrimethylammonium bromide and the addition of organic modifiers to the running buffer (organic solvents, cyclodextrins, urea, cholate) on the parameters of separation and resolution of different secondary metabolites are discussed. The applications of CE to the analysis of flavonoid aglycones and glycosides, phenolic acids, quinones, coumarins, alkaloids, capsacinoids, glucosinolates, polyamines, monoterpenes, diterpenes, phytoecdysteroids, cardiac glycosides and saponins are shown. It is concluded that CE is a very promising analytical technique in the analysis of plant secondary metabolites, and it will become an indispensable tool, together with HPLC and gas liquid chromatography, in phytochemical laboratories since these techniques are in many ways complementary, and problems that are difficult to solve by HPLC can often be solved using CE.