An electronic endoscope system, which is adapted to observe a fluorescence image of autofluorescence emitted from a body cavity wall irradiated with excitation light, includes a controller that controls a light source apparatus to alternately introduce either white light or excitation light into a light guide while taking a normal color image and the fluorescence image, and controls an image signal generating system to generate normal color image signals and fluorescence image signals. The controller further controls a display device to display a still fluorescence image in a first window defined on a displaying area thereof based on the fluorescence image signals which have been generated when a still image switch is turned ON during the time to take the fluorescence image, and simultaneously to display a moving normal color image in a second window defined on a displaying area thereof based on the normal color image signals generated every time the body cavity wall is intermittently illuminated with the white light, the first window being larger than the second window.