Microfluidic devices have gained significant scientific interest due to the potential to develop portable, inexpensive analytical tools capable of quick analyses with low sample consumption. These qualities make microfluidic devices attractive for point-of-use measurements where traditional techniques have limited functionality. Many samples of interest in biological and environmental analysis, however, contain insoluble particles that can block microchannels, and manual filtration prior to analysis is not desirable for point-of-use applications. Similarly, some situations involve limited control of the sample volume, potentially causing unwanted hydrodynamic flow due to differential fluid heads. Here, we present the successful inclusion of track-etched polycarbonate membrane filters into the reservoirs of poly(dimethylsiloxane) capillary electrophoresis microchips. The membranes were shown to filter insoluble particles with selectivity based on the membrane pore diameter. Electrophoretic separations with membrane-containing microchips were performed on cations, anions, and amino acids and monitored using conductivity and fluorescence detection. The dependence of peak areas on head pressure in gated injection was shown to be reduced by up to 92%. Results indicate that separation performance is not hindered by the addition of membranes. Incorporating membranes into the reservoirs of microfluidic devices will allow for improved analysis of complex solutions and samples with poorly controlled volume.