Microchip electrophoresis has become a mature separation technique in recent years. Compared to agarose gel electrophoresis, which is commonly used for DNA separation, microchip electrophoresis has several advantages such as automation, fast analysis speed and minimum sample requirement. For the fabrication of electrophoretic microchips, silica-based and polymer-based materials are two commonly used substrates. Among the polymer-based materials, poly(methyl methacrylate) (PMMA) substrate can be wire-imprinted in a common laboratory to form microfluidic channels without expensive fabrication facilities. Moreover, the neutral hydrophilic surface chemistry of PMMA allows direct DNA separation to be performed on bare microchips without the tedious surface modifications that are normally required for silica-based materials. This chapter presents an imprinting method for fabricating PMMA microchips as well as the on-chip assay for performing electrophoretic DNA separation on the fabricated microchip.