The baseline separation of eight saturated and unsaturated fatty acids of commercial interest was achieved in 15 min by counter-electroosmotic flow capillary zone electrophoresis (CZE), using dimethyl-beta-CD as a buffer additive. The background electrolyte consisted of 10 mM Tris-5 mM p-anisate (pH 8.1) and 1 mM dimethyl-beta-CD in a methanol-water (50:50, vol/vol) mixture. The presence of the cyclodextrin (CD) led to differential migration of critical pairs (i.e., fatty acids of common equivalent chain length or positional isomers). The absence of a highly absorbing chromophore moiety was circumvented through the use of p-anisate as a chromogenic co-ion in the carrier electrolyte. The conditions for indirect absorbance detection were optimized by taking into account the detector linearity and the spectral properties of both analytes and chromophore. A number of parameters influencing the resolution were also discussed, including overloading phenomenon and electroosmotic flow velocity modulation. Quantitative aspects of the method were tested through the analysis of three crude vegetable oils.