A micromachined fluorescence detector has been developed in which an optical interference filter is monolithically integrated and patterned on an amorphous silicon photodiode. The detector can be combined with an excitation light source and the limit of detection is as low as 7 nM of fluorescein concentration. We have also succeeded in the separation and detection of DNA fragments with a high speed, a high sensitivity and a high separation efficiency, using a compact device combining the micromachined fluorescence detector and a microfluidic electrophoresis chip (Figure). This technology will constitute a basic platform to realize compact diagnostic devices, enabling high-speed point-of-care analysis of DNA, RNA, proteins, saccharide chains, etc.