The molecular imprinting technique was first introduced into the microchannel of a microfluidic device to form in situ the imprinted polymer for fast enantioseparation of chiral compounds. The molecularly imprinted polymer (MIP) was in situ chemically polymerized on the microchannel wall using acrylamide as the functional monomer and ethylene glycol dimethacrylate as the cross-linker, and characterized by scanning electron microscopy, atomic force microscopy, and infrared spectroscopy. Under the optimized conditions, such as optimal preparation of MIP, composition and pH of mobile phase, and separation voltage, the model enantiomers, tert-butoxycarbonyl-D-tryptophan (Boc-D-Trp) and Boc-L-Trp, could be baseline separated within 75 s. The linear ranges for amperometric detection of the enantiomers using carbon fiber microdisk electrode at +1.2 V (vs Ag/AgCl) were from 75 to 4000 microM and 400 to 4000 microM with the detection limits of 20 and 140 microM, respectively. The MIP-microchip electrophoresis provided a powerful protocol for separation and detection of Boc-Trp enantiomers within a short analytical time. The molecular imprinting on microchannel wall opens a promising avenue for fast enantioscreening of chiral compounds.