Detection of fluorescent microarray slides can be divided into two categories: one is confocal scanning detection in which a photomultiplier tube is used as fluorescence sensor, and the other is flood illumination of the entire microarray slides and uses a Peltier cooled CCD as fluorescence sensor. CCD can afford high quantum efficiency, simultaneous illumination and detection of multiple pixels, and easy mechanical design, but its dynamic range and sensitivity are not as good as those of photomultiplier tube. At the same time, the Peltier cooled CCD camera is much more expensive than a high performance photomultiplier tube. Confocal scanning provides high dynamic range, good sensitivity and high signal-to-noise ratio, but the system design is difficult when considering rapid scanning speed, high resolution and large numerical aperture. There are three typical confocal scanning apparatuses which are mechanical scanning, optical scanning and optical-mechanical scanning. Their scanning mechanism, advantage and disadvantage are analyzed respectively. With the former understanding, a new optical-mechanical scanning apparatus is described in detail. It employs two lasers to excite the Cy3 and Cy5 fluorophores on the microarray slides. The emitted fluorescent signal is detected using a photomultiplier tube sequentially. One dimension scanning of the slides is performed by a telecentric f-θ objective with a moving coil optical scanner; the other dimension is scanned through a stepping motor driving a precision guidance. This apparatus is low-noise, economical and fast in scanning speed.