The combination of two highly attractive technologies in analytical chemistry, namely molecular imprinting and capillary electrochromatography, is reviewed. Molecular imprinting represents an approach to incorporate affinity binding sites for one or a class of target molecules in network polymers whereas capillary electrochromatography is a technique that profits from the high separation efficiency of electrodriven separations and the high selectivity and capacity available with liquid chromatography. The review discusses and compares the various approaches taken, to combine these concepts aiming at robust, reproducible and easily available capillary-based affinity separation media.