A mass spectrometer capable of obtaining a clear microscopic observation image with high spatial resolution in real time, even during a mass analysis, without affecting the analysis is provided. An aperture 1a is formed in a stage 1 on which a sample plate 2 to be placed. The sample plate 2 is transparent or translucent. A microscopic observation unit, including an observation optical system 20 and a CCD camera 21, is provided below the stage 1 to observe the reverse side of the sample 3 through the aperture 1a of the stage 1 as well as the transparent sample plate 2. The observed image is displayed on the screen of a display unit 27. If the sample 3 is a slice of biological tissue, the sample image taken from the reverse side will be substantially the same as an image taken from the obverse side.