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A simple, novel assay for pathogen diagnosis was implemented on a new integrated microfluidic system using a nanogold modified DNA probe and vancomycin conjugated magnetic beads. The developed microfluidic device was fabricated by microfluidic technology and composed of many micro-modules. The pneumatically-driven, suction-type micropump, microvalves, microchannels and loading chambers were integrated on a single chip to automate the entire diagnosis process. The bacteria were captured by vancomycin conjugated magnetic beads and hybridized with specific nanogold probe. The diagnostic results were determined simply with color change of nanogold by visually bare-eye observation and may be detected optically if necessary. The whole analytic processes only need 25 min from sample and reagent added to results obtained. The developed platform may provide a promising tool for fast diagnosis of bacterial infections.