In this work, a capillary zone electrophoretic methodology using UV indirect detection (224 nm) for the analysis of fatty acids (FAs) in saponified oils is proposed. The electrolyte consisted of a 5 mmol l(-1) phosphate buffer, pH 7. containing 4 mmol l(-1) sodium dodecylbenzenesulfonate (SDBS) as chromophore, 4 mmol l(-1) dimethyl-beta-cyclodextrin and 45% acetonitrile (ACN). The composition of the electrolyte was optimized by a 2(3) factorial design with triplicate at the central point. The design established practical concentration boundaries for SDBS and ACN. In a defined concentration range of 2-4 l(-1), SDBS can certainly be used as a chromophore for indirect detection without imparting excessive baseline noise. For ACN, a suitable interval of 45-55% was found to enhance FAs solubilization without overflowing the system with bubble formation and current interruption. Additionally, the design revealed the importance of dimethyl-beta-cyclodextrin in the resolution of difficult pairs and its function as a solubilizing agent for long chain FAs. At the optimized conditions, nine FAs from C10 to C20, including mono- di- and tri-unsaturated C18 fatty acids were baseline separated in less than 10 min. The proposed method was applied to the separation of FAs in edible oils and polyunsaturated fatty acid enriched margarine. Additionally, spectral monitoring at 206 nm was used to confirm peak identity in the samples.