CE is a family of electrokinetic separation techniques that separate compounds based upon differences in electrophoretic mobilities, phase partitioning, pI, molecular size, or a combination of one or several of these properties. CE has been used in several modes to analyze and characterize a wide variety of analytes from simple inorganic ions, small organic molecules, peptides, proteins, nucleic acids to virus, microbes and particles. Food consists of a complex mixture of a variety of components, many of which are biologically active. Components classified as "nutrients" are essential for growth, maintenance, and repair of the body. Other food constituents, typically occurring in small quantities, are classified as "biologically active substances" and they have beneficial or harmful effects on human health. There are two types of biologically active substances in food - naturally occurring and food additives. The bioactive compounds of food that will be mentioned in this review are inorganic and organic acids, amino acids, vitamins, phenolic compounds, biogenic amines, antinutrients, toxins, etc. This review is focused on the application of CE with hydrodynamically closed system (suppression of EOF) for the analysis of the above-mentioned compounds. CE can be an alternative method to HPLC or other methods for analysis of bioactive compounds in food. The main advantages of CE are low running cost (at least ten times than HPLC) and consideration to environment (hundreds of microliters of diluted water based electrolyte per analysis).