AbstractCapillary electrophoretic methods with normal and reversed electroosmotic flows (EOF) and indirect UV detection were developed for the separation of fatty acids. Rapid separation of acids up to C12 was achieved via reversed EOF using 30% acetone, a cationic surfactant and 3,5‐dinitrobenzoic acid as carrier electrolyte. Analysis of acids up to C18 was feasible by normal EOF with 60% acetonitrile and trinitrobenzenesulfonic acid as carrier. Also investigated was the influence of the concentration of various organic solvents on the magnitude and direction of the EOF and on the solubility of the fatty acid solutes. The reversed EOF method was applied to the analysis of acids in fat hydrolysates.