Molecularly imprinted polymers (MIPs) are actively being developed as a practical tool for affinity chromatographic supports. From the viewpoint of separation science, capillary electrochromatography (CEC) might be one of the more promising chromatographic techniques to be used in combination with the MIPs. However, up to the present, very little MIP work has involved CEC. This review gives a full overview of MIP including current trends in MIP, methods for the characterization of MIP, and methods for the preparation of MIP with particular emphasis on application of the resulting materials in CEC. To prepare MIPs with selectivity predetermined for a particular substance or group of structural analogues is an important factor for the development of a new format of CEC. From the fundamental research with the batch method, a better knowledge of imprint formation and imprint recognition will be helpful for expanding the application area of the combination of MIPs with CEC.