Automatic gain control is provided for a confocal imaging system to improve the quality of images produced by the system. The confocal imaging system utilizes an illumination source, such as a laser, to produce illumination which enables imaging of an object. The automatic gain control is provided by an automatic gain controller which operates in accordance with the counted number of pixels which are too bright, the counted number of pixels which are too dim, and the counted total number of pixels, or in accordance with the average value of pixels, of each two-dimensional frame of the images from the confocal imaging system to control the intensity of the illumination source. The automatic gain controller may be operative over either the entire frame, or a region thereof.