This chapter provides an overview of the application of capillary electromigration techniques, particularly capillary electrophoresis-mass spectrometry (CE MS), in metabolomics. Compared with other metabolomics platforms, CE MS offers a number of advantages, including high sensitivity and ability to separate most charged metabolites. Therefore, it is well suited for the analysis of intermediate metabolites in energy metabolism, such as glycolysis, pentose phosphate pathway and tricarboxylic acid (TCA) cycle, which are mostly negatively charged. First the technical aspects of CE MS are covered, including CE separation modes, MS types, interface and microfluidics systems and data analysis strategies. Subsequently, applications of CE MS in targeted and non targeted metabolomics are described in detail.