A confocal observation system, comprising, an image acquisition unit for acquiring optical cross sectional images of a three-dimensional specimen, a three-dimensional image construction unit for constructing a three-dimensional image from the optical cross sectional images acquired by the image acquisition unit, a specification unit for specifying a desired three-dimensional region in the three-dimensional image constructed by the three-dimensional image construction unit, and a region acquisition unit for acquiring a cross sectional region to be irradiated with excitation light or stimulation light based on the three-dimensional region specified by the specification unit, wherein the excitation light or the stimulation light irradiates a region in the three-dimensional specimen corresponding to the cross sectional region acquired by the region acquisition unit.