There is a continuing drive in microfluidics to transfer microchip systems from the more expensive glass microchips to cheaper polymer microchips. Here, we investigate using polyelectrolyte multilayers (PEM) as a coating system for PMMA microchips to improve their functionality. The multilayer system was prepared by layer-to-layer deposition of poly(diallyldimethylammonium) chloride and polystyrene sulfonate. Practical aspects of coating PMMA microchips were explored. The multilayer buildup process was monitored using EOF measurements, and the stability of the PEM was investigated. The performance of the PEM-PMMA microchip was compared with those of a standard glass microchip and a PEM-glass microchip in terms of EOF and separating two fluorescent dyes. Several key findings in the development of the multilayer coating procedure for PMMA chips are also presented. It was found that, with careful preparation, a PEM-PMMA microchip can be prepared that has properties comparable - and in some cases superior -to those of a standard glass microchip.