We have demonstrated a chip-based microfluidic device suitable for rapid and high-throughput DNA separation and purification for downstream analysis. The glass-based device incorporates a transverse free-flow isotachophoresis (tFF-ITP) that overcomes the volume limitations of CE approaches, and allows continuous sample processing in contrast to batch-mode solid-phase extraction (SPE). The device is able to focus DNA at flow rates up to 100 uL/min, and sample conductivity up to 2 mS/cm. Downstream of the chip, 30-40% of DNA from the input sample is recovered as a result of ITP focusing, and preliminary results indicate that this design is able to purify DNA from contaminating species, particularly those that inhibit PCR