An endoscope system is disclosed for detecting fluorescent light emitted in the near-infrared region by a plurality of fluorescent labeling materials introduced into a living tissue.An illumination system generates illumination light in the wavelength range 600 nm-2000 nm which serves as excitation light for the plurality of fluorescent labeling materials, and a detection system that can separately detect different ones of the plurality of fluorescent light emissions that are emitted at different wavelengths from among the plurality of fluorescent labeling materials is provided. The endoscope system may include a conventional-type endoscope having an insertion section, or a capsule endoscope that wirelessly transmits image data. By superimposing the image data obtained using reflected light in the visible region and fluorescent light emitted by the fluorescent labeling materials, improved diagnostic capabilities are provided.