Provided are an endoscope system, a processor device, and a method of operating an endoscope system that can substantially simultaneously and accurately discriminate a plurality of regions having different features.An endoscope system (10) includes a light source unit (20), an image sensor (48), an image acquisition unit (54), a first image generation unit (81), a second image generation unit (82), and a region discrimination unit (84). The light source unit (20) emits a plurality of types of illumination light beams with different wavelengths. The image acquisition unit (54) acquires images corresponding to the respective illumination light beams. The first image generation unit (81) generates a first image (white light image (101)) serving as a base of a display image (121). The second image generation unit (82) generates a second image (bright/dark region discrimination image (112) or the like), using at least one image having a different corresponding wavelength from that of the image used for the generation of the first image. The region discrimination unit (84) discriminates the regions in the observation target, using the second image.
