Capillary electrophoresis-mass spectrometry (CE-MS) has proven to be an important technology for metabolomics studies. Most primary metabolite intermediates contain hydroxyl, amino, carboxyl and phosphate groups and, therefore, are charged, which makes them suitable for CE-MS analysis. The major advantages of CE-MS are its high resolution and the fact that almost any charged metabolite (both cationic and anionic) can be analyzed by only two analytical modes. CE-MS can be readily applied to various kinds of biological samples. This chapter highlights the general CE-MS conditions specifically developed for profiling cationic and anionic metabolites, and also focuses on several biological samples frequently used in medical and biochemical metabolomics, including blood (serum and plasma), urine, tissue, cultured cells and other related samples.