The developments in molecularly imprinted polymer (MIP)-based capillary electrochromatography (CEC) achieved during the past years are reviewed in this article. The MIP is prepared using a templated polymerization reaction and results in a material with a high selectivity towards a predetermined target. The selectivity of the MIP is comparable to that of the biological antibodies, however, the MIP is much more stable and is thus able to withstand extremely harsh conditions in terms of pH, temperature, and organic solvents. The high selectivity and stability of the MIP made it an interesting candidate for application as stationary phase sorbent in chromatography. However, due to slow kinetics the efficiency of the early MIP columns, which were predominantly applied in high-performance liquid chromatography (HPLC), were limited. The use of CEC was thought to improve the efficiency of the MIP-based separation system. The small dimensions of the capillary format employed in CEC have put demands on the polymer systems which have resulted in the development of many different polymer formats. Thus, this need for novel MIP formats for applications in CEC has contributed a lot to the general development of MIP formats as well as to the knowledge in MIP synthesis and characteristics.