A microscope system has a stage on which an observation sample, including an observation object and a transparent member, is to be placed. An objective lens is placed to face the observation sample placed on the stage, and a focusing unit moves at least one of the stage and the objective lens to perform a focusing operation. An autofocus unit controls a focusing driving unit by a so-called Through-the-Lens: TTL system. After autofocus is performed for the transparent member by the autofocus unit, the focusing driving unit makes at least one of the stage and the objective lens move by a predetermined constant amount.