Hydrogenated amorphous silicon (a-Si:H) pin photodiodes are used as fluorescence sensors for microfluidic analysis devices. A hybrid-integrated sensor consisting of a half-ball lens, a ZnS/YF 3 multilayer optical interference filter with a pinhole, and an annular a-Si:H photodiode is developed that allows the laser excitation to pass up through the central aperture in the photodiode. Using this integrated device, the limit of detection for fluorescein flowing in a 50-μm deep channel is 17 nM (S/N=3) and DNA fragment sizing and chiral analysis of glutamic acid are successfully performed. The a-Si:H sensor exhibits high sensitivity at the emission wavelengths of commonly used fluorescent dyes and is readily microfabricated and integrated at low cost making it ideal for portable microfluidic bioanalyzers.