This review article is a comprehensive survey of capillary electrophoresis methods developed for the measurement of short-chain organic acids and inorganic anions in a wide variety of matrices, such as food and beverages, environmental, industry, and other applications, as well as clinical applications in body fluids such as urine, plasma or cerebrospinal fluid. Details of sample pretreatment and of electrophoretic conditions have been collected in tables, arranged by the type of matrix. Strategies employed for method development for the analysis of these compounds by capillary electrophoresis in real samples are discussed.