This review article addresses the different capillary electrophoretic methods that are being used for the study of both short-chain organic acids (including anionic catecholamine metabolites) and fatty acids in biological samples. This work intends to provide an updated overview (including works published until November 2004) on the recent methodological developments and applications of such procedures together with their main advantages and drawbacks. Moreover, the usefulness of CE analysis of organic acids to study and/or monitor different diseases such as diabetes, new-borns diseases or metabolism disorders is examined. The use of microchip devices and CE-MS couplings for organic acid analysis is also discussed.