We are developing a variety of microsystems for the separation and detection of biological samples. At the heart of these systems, inexpensive polymer microfluidic chips carry out sample preparation and analysis. Fabrication of polymer microfluidic chips involves the creation of a master in etched silicon or glass; plating of the master to produce a nickel stamp; large lot chip replication by injection molding; precision chip sealing; and chemical modification of channel surfaces. Separation chips rely on insulator-based dielectrophoresis for the separation of biological particles. Detection chips carry out capillary electrophoresis to detect fluorescent tags that identify specific biological samples. Since the performance and reliability of these microfluidic chips are very sensitive to fluidic impedance, electromagnetic flux, and zeta potential, the microchannel dimensions, shape, and surface chemistry have to be tightly controlled during chip fabrication and use. This paper will present an overview of chip design, fabrication, and testing. Dimensional metrology data, surface chemistry characterization, and chip performance data will be discussed in detail.