A laser scanning microscope apparatus includes an irradiation unit including an objective lens, a photodetector unit, an XY-scanning unit, and a Z-scanning unit. The irradiation unit focuses a laser beam with the objective lens to a specimen. The photodetector unit detects light generated from a position irradiated with the laser beam focused. The XY-scanning unit scans the laser beam in an X-direction perpendicular to an optical axis of the objective lens and in a Y-direction perpendicular to the optical axis and the X-direction. The Z-scanning unit scans the laser beam in a Z-direction parallel to the optical axis. When acquiring XY-two-dimensional image data by detecting the light while scanning the irradiated position in the X-direction and the Y-direction, the apparatus detects the light while scanning the irradiated position also in the Z-direction.