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This paper reports a planar flow cytometer for the detection of fluorescent particles using evanescent waves based on the liquid total internal reflection (L-TIR). This on-chip flow cytometer is able to form the evanescent waves on the interface between liquids which can be used to detect the fluorescent particles in nanosize with high speeds. The total internal reflection is formed to generate the evanescent waves by the geometry of the liquid interface which is defined by the structure of the device. The particles are injected and focused by the hydrodynamic method which makes the particles go through the optical detection area shined by the exciting laser one by one. This method has been proven to be a fast and effective method to analyze fluorescent particles or cells with the exciting light in the depth of several hundred nanometers.