Capillary electrophoresis-mass spectrometry (CE-MS) is increasingly used for the targeted and untargeted analysis of metabolites in biological samples. CE-MS is particularly useful for the profiling of highly polar metabolites without the need for derivatization and/or extensive sample preparation. This overview covers reported studies in which CE or CE-MS was used with direct MS, gas chromatography (GC)-MS, liquid chromatography (LC)-MS, and/or nuclear magnetic resonance (NMR) spectroscopy for the analysis of metabolites. We include an extensive overview of comparative metabolic profiling studies involving multiple analytical techniques, including CE. Tables set out the particular conditions and the characteristics of each study. Furthermore, we discuss and compare the results of these studies using selected examples. Based on the outcomes of the comparative studies, we conclude that CE is highly complementary to the other analytical technologies and can add essential information on the metabolic profile of biological samples.