In the present work, an exhaustive review of the main developments and applications of CE-MS for peptide analysis is given. This review includes the use of different CE separation modes, MS analyzers, capillary coatings, preconcentration techniques, on-chip applications as well as other different multidimensional strategies for peptide analysis. Key applications are critically discussed and relevant works published from January 2000 to May 2007 are summarized including information concerning the type of sample, CE-MS parameters as well as some figures of merit of the different CE-MS procedures developed for peptide analysis and peptidomics.