This work provides an updated overview (including works published till June 2004) on the principal applications of capillary electrophoresis-mass spectrometry (CE-MS) together with their main advantages and drawbacks in food science. Thus, analysis of amino acids, peptides, proteins, carbohydrates, or polyphenols by CE-MS in different, foods is reviewed. Also, other natural compounds (e.g., alkaloids) and toxins analyzed by CE-MS in foods are revised. Moreover, exogenous substances with a potential risk for human health (e.g., pesticides, drugs) detected in foods by CE-MS are included in this work. The usefulness of CE-MS for food analysis and the information that this coupling can provide in terms of processing, composition, authenticity, quality, or safety of foods is also discussed.