An overview of the application of CE-MS in the field of metabolomics is provided. The study of endogenous low-molecular-weight compounds in biological samples is known as metabolomics. CE-MS has proven to be an effective technique for profiling polar metabolites in biological samples. This review discusses the application of various CE separation modes, capillary coatings, MS analyzers, sample preparation techniques, and data analysis methods . The use of CE-MS in metabolomics research is demonstrated by analysing bacterial extracts, plant extracts, urine, plasma, and cerebrospinal fluid samples. The relevant CE-MS metabolomics studies published between 2000 and 2008 are tabulated, including information on sample type and pretreatment and MS detection mode. Future developments are discussed, including the use of alternative ionization techniques, coupled separation systems, and the potential of microchip CE systems for metabolomics.