In the present study, the enantiomeric forms of hydrophobic amino acids (L-tryptophan, L-tyrosine, and L-phenylalanine) were separated by molecularly imprinted capillary columns (MICC) via Capillary Electrochromatography (CEC) for the first time. The monomer ratio, crosslinker ratio, template molecule ratio, the porogen ratio and type, polymerization time, and also the effect of temperature were examined to increase the permeability properties of MICC. FTIR, SEM and BET analyses were realized for the characterization of MICC. The effect of the electric field, organic solvent ratio, and pressure were carried out experimentally to determine the optimum conditions. The separation performances of MICC and the non-imprinted capillary columns (NICC) were compared electrochromatographically.