A motor-operated microscope system has a motor-operated microscope section including an illumination optical system, an electric stage, an image forming optical system having an objective lens and an image forming lens, and an image pickup device; a housing; a control device having a screen display and an arithmetic processing section; and software displaying an operating condition setting screen of the motor-operated microscope section on the screen display and controlling an operation of the motor-operated microscope section in accordance with a set condition. The operating condition setting screen has, on one screen, a setting section for an exposure condition with the image pickup means; a setting section for a focusing condition with the objective lenses; an objective interchange setting section; a setting section for wavelength and luminance of illumination light; a setting section for an image pickup range; a display section for a picked-up image; and an operation commanding section for the motor-operated microscope section.