Nanoparticles are widely used in capillary electrophoresis as stationary phases adsorbed on the internal capillary walls for the separation and concentration of analytes in capillary electrochromatography. The fastest and simplest approach for the formation of coatings is a physical adsorption of nanoparticles. Nevertheless, the formed coatings frequently possess low stability. The layer-by-layer approach for the formation of stabile and dense coating of internal capillary walls based on negatively charged nanosized cation-exchanger was proposed. The method included the sequential alteration of appositively charged layers of nanosized ion-exchangers. The proposed “anion-exchanger - cation-exchanger” bilayer coating possesses high stability in wide pH range (2-10) and provides up to 120 analyses without the need of re-coating. The coating was applied for the separation and on-line concentration of catecholamines and amino acids in capillary electrochromatography mode. High efficiencies were achieved (N = 450-720 th. t.p./m and N = 400-520 th. t.p./m for cathecholamies and amino acids, respectively), while the analysis time was significantly decreased. It was established, that high concentration of negatively charged functional groups on the capillary surface led to the increase of stacking efficiency factors due to the interactions between analytes and functional groups of the modifier on the capillary walls. It contributed to the 2-4 times reduced detection limits (LODs) of analytes compared to the mono-layer coatings (LODs of catecholamines = 3-4 ng/mL, LODs of amino acids = 40-100 ng/mL).