A molecularly imprinted polymer has been successfully utilized as nanoreactors for Huisgen 1,3-dipolar cycloaddition of azides and alkynes, leading to high product regioselectivity and kinetic acceleration.The MIP nanoreactors also showed remarkable selectivity toward the reactant structures, so that the “best fit” product was mostly amplified during the reaction. In contrast to previously reported regioselective MIPs, the present imprinted cavities bind reactants by means of only noncovalent molecular interactions, the same as that normally involved in biological systems. The results support the concept of drug “cloning” that further extends both the anti-idiotypic imprinting and in-cavity synthesis approaches into the modern drug discovery area.