The laser scanning microscope system includes a microscope unit including at least one laser source, at least a microscope main body, a stage on which a sample is laid, an objective lens which converges a light from a sample to form a parallel light, and a first image formation lens which converges the parallel light from the objective lens, and at least one light detector which detects light from the sample through a confocal pinhole, and a scanning unit disposed attachably/detachably with respect to the microscope main body, the scanning unit includes a optical scanning device which scans a laser light from the laser source, a pupil projection lens and a second image formation lens arranged so that the optical scanning device and a pupil position of the objective lens are optically conjugated, and at least one photodetector which detects light from the optical scanning device through a confocal pinhole, and the scanning unit is attached to the microscope main body so that an optical axis of an optical path branched by a deflection part disposed between the objective lens and the first image formation lens is aligned with that of the optical path of the second image formation lens.