Microfabricated lab-on-a-chip systems are ideal for rapid on-the-spot detection of bacterial or viral pathogens. For example, on-chip quantitative polymerase chain reaction (PCR) assays utilizing nanoliter-scale quantities of reagents and sample materials have been demonstrated. For a truly portable device, however, the entire upstream sample purification procedure would also need to be integrated. This would require the incorporation of a nucleic acid purification step prior to detection with the PCR. We describe efforts to adapt to a microchip format a standard nucleic acid purification technique based on the binding of nucleic acids to the surface of silica particles in the presence of a chaotropic salt solution. We demonstrate through experiments the relevant parameters to vary in designing such a nucleic acid purification microchip and how one would optimize such a device to provide nucleic acid of sufficient concentration and purity for PCR amplification. The feasibility of purifying RNA from a clinical sample, which is relevant for the detection of pathogens such as bird flu, is demonstrated.