A microscope apparatus that can observe into the interior of a specimen and that can apply an optical stimulus over a wide area within a short period of time is provided. The microscope apparatus comprises at least one observation scanning optical system including a laser light source for emitting observation laser light, an objective lens, and a scanning optical system for two-dimensionally scanning the observation laser light in a predetermined examination plane of the specimen via the objective lens; and at least one stimulus optical system which includes a lamp light source for emitting light having a wavelength used for optical stimulation and which irradiates the specimen with the light emitted from the lamp light source.