An overview of the use of CE-MS in the field of metabolomics is provided. Metabolomics is concerned with the comprehensive analysis of endogenous low-molecular-weight compounds in biological samples. CE-MS has demonstrated to be a powerful technique for the profiling of polar metabolites in biological samples. This review covers the use of various CE separation modes, capillary coatings, MS analyzers, sample preparation techniques, and data analysis methods used in CE-MS for metabolomics. The applicability of CE-MS in metabolomics research is illustrated by giving examples of the analysis of bacterial extracts, plant extracts, urine, plasma, and cerebrospinal fluid samples. The relevant CE-MS metabolomics studies published between 2000 and 2008 are presented in tabular form, including information on sample type and pretreatment and MS detection mode. Future developments with regard to the use of alternative ionization techniques, the use of coupled separation systems and the potential of microchip CE systems for metabolomics are discussed.