An electronic endoscope system includes an electronic endoscope having a CMOS image sensor on the tip of an insertion section, a light source device for illuminating the interior of a patient's body, and a processing device for reading out image signals from the CMOS image sensor. The electronic endoscope system can operate with a standard imaging mode and a special imaging mode. When the time taken to read out the image signals from all the pixels in the standard mode is defined as T, the light source device in the special imaging mode emits illumination light in every first half period T/2 while switching a wavelength of the illumination light between two different wavebands. In every second half period T/2, the processing device reads out the image signals from the half of the pixels.