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This review focuses on the application and implication of CEC for natural product analysis, with special emphasis on reports published after 2005. The basic concepts and principles of CEC are outlined, and the techniques advantages and disadvantages are discussed in context with the available stationary phase format. Special attention is given to the application of packed beds and monolithic formats of CEC with both silica-based and in situ formed polymeric stationary phases. The most promising applicative platforms are presented and their potential for natural product analysis is discussed.