Fluorescence generated at a lesion is distinguished from fluorescence generated at portions other than the lesion, and thus, observation is performed by using only the fluorescence generated at the lesion. Provided is a fluorescence observation apparatus including a light radiating portion that radiates excitation light onto an examination subject; a fluorescence-distribution acquiring portion that acquires an intensity distribution of fluorescence generated at the examination subject due to irradiation with the excitation light from the light radiating portion; and a non-target-region excluding portion that, in the fluorescence-intensity distribution acquired by the fluorescence-distribution acquiring portion, excludes regions in which a spectrum in a specific wavelength band has changed due to a specific biological component whose concentration in a lesion is lower than in other portions.