A 2-D method was developed for separation of phenolic acids and flavone compounds combining LC with MEKC. The effect of substituted neutral and anionic CD additives to the background electrolyte on the quality of MEKC separation was investigated. The best selectivity of the MEKC separation was achieved in 25 mmol/L borate background buffer at pH 9.05 with the addition of 10 g/L SDS and 1.85 g/L heptakis (6-O-sulfo)-beta-CD. These conditions were used in the second dimension of 2-D combination of LC and MEKC separation in combination with a PEG column in the first dimension, providing the best orthogonality (the lowest degree of correlation between the selectivity of separation) in the two dimensions. A CE autosampler was employed as the interface between LC and MEKC steps based on automated fraction collection before the re-analysis of the collected LC fractions in the second, MEKC dimension. The 2-D method under optimized conditions was applied for the separation of natural antioxidants in the samples of green tea.