A microscope system and an autofocus method capture a subject at a specified time interval through an optical image forming system while relatively moving a stage loaded with the subject and the optical image forming system of the microscope; calculate a contrast value indicating a high and low contrast of a captured observation image; detect a maximum contrast image whose calculated contrast value is maximum in a plurality of performed observation images; detect the relative position of the stage and the optical image forming system; perform a correcting process of moving the detected relative position corresponding to the detected maximum contrast image by a specified value in a direction opposite the direction of the relative movement; and bring focus using the corrected relative position as a focal point.