An endoscope apparatus for generating an image of a site to be observed containing a fluorescent substance that is excited by excitation light in a red color region and emits fluorescence in a near-infrared region, comprising: a light source section configured to simultaneously emit to the site to be observed, excitation light in a red color region and reference light in a predetermined wavelength band which is a blue color region or a green color region for generating reflected light from the site to be observed; an excitation light cut filter section configured to have optical characteristics that shut off the excitation light and allow light in a wavelength band other than the excitation light to substantially pass therethrough; characterized by a color filter section provided with a first filter configured such that transmittance in a region from the red color region to the near-infrared region is relatively higher than transmittance in other wavelength bands, and a second filter configured such that transmittance in the predetermined wavelength band of the reference light is relatively higher than the transmittance in the other wavelength bands; an image pickup section including pixels for generating an image pickup signal by picking up an image of light which is among return light emitted from the site to be observed according to emission of the excitation light and the reference light to the site to be observed and which passed through the excitation light cut filter section and the first filter, and pixels for generating an image pickup signal by picking up an image of light which is among the return light and which passed through the excitation light cut filter section and the second filter; and an image processing unit configured to perform processing to acquire a first image obtained by separating a first color component corresponding to the fluorescence, image which is picked up after passing through the excitation light cut filter section and the first filter, from respective color components included in the image pickup signal generated by the image pickup section, and a second image obtained by separating a second color component corresponding to the reference light, image which is picked up after passing through the excitation light cut filter section and the second filter, from the respective color components. a light source section configured to simultaneously emit to the site to be observed, excitation light in a red color region and reference light in a predetermined wavelength band which is a blue color region or a green color region for generating reflected light from the site to be observed; an excitation light cut filter section configured to have optical characteristics that shut off the excitation light and allow light in a wavelength band other than the excitation light to substantially pass therethrough; characterized by a color filter section provided with a first filter configured such that transmittance in a region from the red color region to the near-infrared region is relatively higher than transmittance in other wavelength bands, and a second filter configured such that transmittance in the predetermined wavelength band of the reference light is relatively higher than the transmittance in the other wavelength bands; an image pickup section including pixels for generating an image pickup signal by picking up an image of light which is among return light emitted from the site to be observed according to emission of the excitation light and the reference light to the site to be observed and which passed through the excitation light cut filter section and the first filter, and pixels for generating an image pickup signal by picking up an image of light which is among the return light and which passed through the excitation light cut filter section and the second filter; and an image processing unit configured to perform processing to acquire a first image obtained by separating a first color component corresponding to the fluorescence, image which is picked up after passing through the excitation light cut filter section and the first filter, from respective color components included in the image pickup signal generated by the image pickup section, and a second image obtained by separating a second color component corresponding to the reference light, image which is picked up after passing through the excitation light cut filter section and the second filter, from the respective color components.