On-site detection methods for DNA have been demanded in the pathophysiology field. Such analysis requires a simple and accurate method, rather than high-throughput. This report describes a novel microfluidic analysis method and its application for simple sequence-selective DNA detection with high accuracy. A microchannel offers superior controllability of fluids. The method uses a microchannel device with a serpentine structure. This method does not require immobilization of probe or target DNA: solutions are merely injected into the microchannel and all reactions occur in the liquid phase. Such features might lower the experimental error and difference in data by operators.