Microfluidic devices are revolutionary in their ability to use very small quantities of liquid samples and to perform biochemical analyses with unprecedented speed. Toward the goal of a lab-on-a-chip that integrates a series of analysis steps and analytical components into a single microfluidic device, one of the most critical aspects of size reduction is miniaturizing and integrating the fluorescence detection system. We present here details of a new integrated fluorescence detection system. A microfluidic biochemical analysis device is mounted on a compact detection platform that comprises a fluorescence-collecting microlens and micromachined fluorescence detector in which a multilayer optical interference filter is monolithically integrated and patterned on a hydrogenated amorphous silicon (a-Si:H) photodiode. A central aperture in the micromachined a-Si:H fluorescence detector allows semiconductor laser light to pass up through the detector and to irradiate a microchannel of the microfluidic analysis device. Such an optical configuration enables a detachable, reusable, compact module to be constructed for the excitation source and detector. The micromachined a-Si:H fluorescence detector exhibits high sensitivity for practical fluorescent labeling dye, making it ideal for application to portable point-of-care microfluidic biochemical analysis devices.