A microscope system includes a culture unit for holding and cultivating a specimen while maintaining constant temperature and humidity; a stage for holding the culture unit; a first light-converging optical system for converging illumination light emitted from a light source on the specimen; a second light-converging optical system for converging transmitted light that has passed through the specimen; a transmitted-light pinhole provided at a position optically conjugate to the light-converging position of illumination light on the specimen to cut off part of transmitted light converged by the second light-converging optical system; a transmitted-light detector that detects transmitted light that has passed through the transmitted-light pinhole; a moving system for moving the first and second light-converging optical systems, the transmitted-light pinhole, and the transmitted-light detector and the stage relative to each other; a housing that encloses these components and cuts off external light; and a control unit.