This review provides an update of the state-of-the-art of CE-MS for metabolomic purposes, covering the scientific literature from July 2008 to June 2010. This review describes the different analytical aspects with respect to non-targeted and targeted metabolomics and the new technological developments used in CE-MS for metabolomics. The applicability of CE-MS in metabolomics research is illustrated by examples of the analysis of biomedical and clinical samples, and for bacterial and plant extracts. The relevant papers on CE-MS for metabolomics are comprehensively summarized in a table, including, e. g. information on sample type and pretreatment, and MS detection mode. Future considerations such as challenges for large-scale and (quantitative) clinical metabolomics studies and the use of sheathless interfacing and different ionization techniques are discussed.