A micellar electrokinetic chromatography (MEKC) method has been developed for the direct resolution of divinyl ether type of hydrophobic fatty acid isomers. The fatty acid isomers resolved include colneleic acid ICL), colnelenic acid (CLn), 14(Z)-etheroleic acid (14(Z)-EL), 14(Z)-etherolenic acid (14(Z)-Eln), 11(Z)-etheroleic acid (11(Z)-EL), 11(Z)-etherolenic acid (11(Z)-Eln), etheroleic acid (EL) and etherolenic acid (Eln). These fatty acid isomers differ in number, position and spatial arrangement of the double bonds and the position of the ether oxygen. A central composite design was employed for the optimization of the key variables of the separation, namely the concentrations of sodium dodecyl sulfate (SDS) and organic modifiers. The use of micelles combined with an organic modifier in the background electrolyte made it possible to dissolve and separate relatively hydrophobic fatty acid isomers, and to achieve high separation efficiency. Using heptakis-(2,3-dimethyl-6-sulfato)-beta -cyclodextrin (HDMS-beta -CD) as a buffer additive, complete separation of the examined eight divinyl ethers was achieved. Separation efficiencies up to 5 x 10(5) theoretical plates/m were achieved under optimized conditions. Direct UV was applied for detection of the fatty acids. The results were compared with those obtained from high-performance liquid chromatography (HPLC) separation.