1. A fluorescence observation apparatus comprising: an illuminating section that is inserted into a body cavity of a biological organism and that emits excitation light onto an inner wall of the body cavity; an image acquisition section that acquires an image of fluorescence generated by the excitation light emitted from the illuminating section so as to acquire image information; and a counting section that counts the number of fluorescence generation sites on the basis of the fluorescence included in the image information acquired by the image acquisition section, the fluorescence generation sites being generated when a fluorescent probe whose fluorescence characteristic changes by reacting with a molecule existing in an ACF formed on the inner wall of the body cavity is excited or when fluorescent probes whose fluorescence characteristic changes by reacting with a product produced by activation of the molecule is excited.