A micro fluorescent analysis system is proposed using silicon micromachining. GaN blue light-emitting diode (LED) monolithically integrated on a silicon substrate is used as a light source for the fluorescent analysis system. The blue light suits the excitation of several dyes used commonly in fluorescent analysis. Silicon photodiode (Si-PD) that matches the visible and near infrared fluorescent wavelengths of dyes is integrated on a silicon substrate. Polydimethylsiloxane (PDMS) micro-channels are also stacked for flowing dye-sensitized liquid. Therefore, the proposed system is an integrated system that can be composed on a silicon platform, i.e. a bottom layer of Si-PD, a middle layer of GaN-LED on silicon substrate and a top layer of micro PDMS channel. An aperture is opened into the GaN-LED layer by deep reactive ion etching to create a ring-shaped GaN-LED and a through-hole for detection. The light from the ring-shaped GaN-LED in the middle layer excites the dye-sensitized liquid in the top micro-channel layer. The fluorescence emitted from dye is detected by the Si-PD on the bottom layer at an angle larger than 90 degrees from the direction of excitation. Therefore, the detection optics consist basically of a dark-field illumination optical system. In order to evaluate the performance of the integrated system, fluorescence of fluorescein isothiocyanate (FITC) solution flowing in the micro channel is measured. From the measurement, the noise, sensitivity and limit of detection in the fabricated system are evaluated for FITC dye to be 0.57 pA, 1.21 pA μM-1 and 469 nM, respectively. From these results, a compact fluorescence analysis system is demonstrated.