Abstract This article describes the potential of capillary electrophoresis (CE) in metabolomics, which concerns the comprehensive analysis of endogenous low-molecular weight compounds in a biological system. Consequently, metabolomic methods are often developed to separate and to detect as many endogenous metabolites as possible in a single analysis. CE is a very powerful technique for this type of profiling. We demonstrate the applicability of CE in different fields of metabolomics research. We show illustrative clinical, bacterial and plant examples and stress the information that CE systems obtain. We distinguish between targeted and non-targeted metabolomic studies in the bacterial and plant sections. We discuss general aspects of sample preparation of CE for biological samples, and pay special attention to the potential of CE-mass spectrometry in metabolomics. We also discuss future developments with regard to sample preparation and the use of hyphenated systems.