An endoscope apparatus for generating an image of a target site containing a fluorescent substance, including an image pickup section provided with pixels for generating image pickup signals corresponding to a red color region and a band closer to a long wavelength side than the red color region and pixels for generating an image pickup signal corresponding to a band closer to a short wavelength side than the red color region, a light source section emitting to the target site, excitation light for exciting the fluorescent substance and generating fluorescence and reference light for generating reflected light from the target site, and an image processing unit that acquires an image obtained by separating a signal component generated upon receiving the fluorescence from the image pickup signal generated by the image pickup section and an image obtained by separating a signal component generated upon receiving the reflected light.
