Capillary electrophoresis (CE) was introduced as a new analytical technique in the 1970s and rapidly proved to be a powerful tool for the separation and detection of various classes of natural and synthetic compounds. Since the availability of commercially manufactured high-performance instruments, CE represents an interesting alternative to high-pressure liquid chromatography (HPLC), mainly because of its speed and high separation efficiency. In this overview a short description of the basic and widely used CE methods will be given and the applicability of these methods for the analysis of natural products will be discussed. Due to the growing number of publications dealing with CE or CE/MS of secondary plant metabolites, an exhaustive overview of all current applications cannot be given in this contribution. Therefore, the focus of this mini-review will be on the advances and new aspects of recently published CE methods in natural products analysis.