The use of molecularly imprinted polymers polymerized in a capillary for the separation of amino acid enantiomers by electrochromatography is described. The substrate-selective polymers were prepared by using l-phenylalanine anilide as print molecule and methacrylic acid as the functional monomer. The treatment of the inside surface of the capillary, the composition of the polymer and the electrochromatographic running conditions were investigated. This preliminary report demonstrated a novel and simple method for capillary electrochromatographic separations of amino acid enantiomers using molecularly imprinted polymers.