The number of aberrant crypt foci (ACF) can be readily counted without overlooking the existence of ACF to achieve reduced observation time. A fluorescence observation apparatus includes a light source unit inserted into a body cavity of a biological organism and emitting excitation light onto an inner wall of the body cavity; an image acquisition unit that acquires image information by acquiring an image of fluorescence generated when a fluorescent probe whose fluorescence characteristic changes by reacting with a molecule existing in an ACF formed in the inner wall of the body cavity is excited by the excitation light; a position control unit that moves the light source unit and the image acquisition unit relative to the inner wall of the body cavity; and a counting section that counts the number of fluorescence generation sites included in the image acquired by the image acquisition unit.