A microscope apparatus includes: a light source; an illumination optical system configured to illuminate a specimen with light from the light source, the illumination optical system having a spatial light modulation element capable of adjusting a light intensity distribution; an imaging optical system configured to image light from the specimen; a solid-state imaging device configured to generate an image of the specimen based on light from the imaging optical system; and a controller capable of adjusting the spatial light modulation element, the controller being configured to, based on a first image output from the solid-state imaging device when the specimen is illuminated with first illumination light, adjust the spatial light modulation element and illuminate the specimen with second illumination light.