Microemulsion electrokinetic chromatography (MEEKC) was applied to the separation of six catechins and caffeine, the major constituents of the green tea. The developed methods involved the use of sodium dodecyl sulfate (SDS) as surfactant, n-heptane as organic solvent and an alcohol as cosurfactant. The separations were performed under acidic conditions (pH 2.5 phosphate buffer, 50 mM) to ensure good stability of the catechins, with reversed polarity (anodic outlet). The effect of the alcohol nature on the MEEKC selectivity was evaluated; nine alcohols were used as cosurfactant: 1-butanol, tert-butanol, 1-pentanol, 2-pentanol, 3-pentanol, cyclopentanol, 1-hexanol, 2-hexanol, and cyclohexanol. The migration order of (+)-catechin (C), (-)-epicatechin (EC), (-)-epigallocatechin (EGC), (-)-gallocatechin (GC), (-)-epigallocatechin gallate (EGCG), (-)-epicatechin gallate (ECG), caffeine and theophylline was significantly affected by the alcohol used as cosurfactant. Using nine microemulsions, four different selectivities were achieved: A (cyclohexanol); B (2-pentanol, 3-pentanol, 1-hexanol, 2-hexanol); C (1-butanol, 1-pentanol, cyclopentanol); D (tert-butanol). MEEKC methods, based on 2-hexanol and cyclohexanol as cosurfactant were validated and successfully applied to the analysis of catechins and caffeine in commercial green tea products.