A microscope system includes an observation optical system including an objective lens, an XY stage capable of moving an XY plane in an X-axis direction and an Y-axis direction, a first change unit configured to change a slant of the XY plane with respect to an optical axis direction of the objective lens, and a second change unit configured to change a slant of a slide placed on the XY stage with respect to the XY plane. Changing the slant of the XY plane by the first change unit is performed based on a first mark arranged on the XY plane at a position observable by the observation optical system. Changing the slant of the slide with respect to the XY plane by the second change unit is performed based on a second mark arranged on the slide.