A microscope system that shifts a plurality of observation locations that are set upon an observation subject in order onto an optical axis of an objective optical system, and for each of the observation locations, performs photography with an image-capturing device of an observation image of the observation subject a plurality of times as time elapses, includes: a drive unit that drives a stage upon which the observation subject is mounted, and the objective optical system, relative to one another two dimensionally in directions orthogonal to the optical axis; a position detection unit that detects at least one of positions of the stage and the objective optical system; and a correction unit that, based upon position information detected by the position detection unit, performs trimming correction upon a plurality of photographic images that have been photographed at each observation location as time elapses, so that the plurality of photographic images become images of a same observation region that includes the observation location.