Abstract: An optical cone-coupled ICCD system was developed to detect the biochips labeled with fluorescent molecules. The CCD chip and image intensifier were cooled to increase the sensitivity of the system. Based on the analyzed results of the experiment, it is determined that the major background noise comes from the stray light and the fluorescence from the substrate impurities of the biochip, and the sensitivity of the system is limited by the objective lens for imaging. The background noise can be effectively reduced and the detection sensitivity can be improved by using a substrate with less fluorescent impurities, such as a quartz substrate.