To avoid collision between an objective lens and a stage, in a microscope system having a general object lens and stage.

The microscope system includes: the stage movable in an XY direction; the objective lens disposed below the stage; a movable member holding the objective lens and movable vertically; a storage unit for storing information about the stage and objective lens; and a controller for exerting control such that when the stage is moved, with reference to the information stored in the storage unit, the stage is cumulatively moved by repeating the step of making a comparison between the range, in which the stage is movable to the movable member and the stage does not contact the objective lens, and the position, to which the stage has been moved by a predetermined distance, and the step of moving the stage by the predetermined distance when the stage does not contact the objective lens even if the stage is moved by the predetermined distance, and such that when the stage contacts the objective lens if the stage is moved by the predetermined distance, the stage is not moved.