In this work, I present capillary electrophoresis as a complementary separation technique to high-performance liquid chromatography and gas chromatography for the separation of metabolite samples. In particular, I focus on demonstrating the usefulness of capillary electrophoresis for performing rapid separations lasting less than ten minutes. Capillary electrophoresis is especially well suited for the analysis of small, polar metabolites because of its high resolution and aqueous running conditions. In addition, I demonstrate and investigate new technologies for coupling capillary electrophoresis to mass spectrometry and ionizing molecules for mass spectrometric analysis and detection. As a final demonstration of the capability of capillary electrophoresis to rapidly analyze the metabolome, I present a study of the metabolism of early Xenopus laevis embryos.