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A novel bacterial DNA sample preparation device for molecular diagnostics has been developed. Based on optimized conditions for bacterial adhesion, surface-modified silicon pillar arrays for bacterial cell capture were fabricated and their ability to capture bacterial cells was demonstrated. The capture efficiency for bacterial cell, E. coli, in buffer solution was over 90% with a flow rate of 400 mulscr/min. Moreover, the proposed method captured E. coli cells present in 50% whole blood effectively. The captured cells from whole blood were then in-situ lyzed on the surface of the microchip and the eluted DNA was successfully amplified by qPCR. These results demonstrate that the full process of pathogen capture to DNA isolation from whole blood could be automated in a single microchip.