We have developed a mass microscope in which a microscope is combined with high-resolution matrix assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS). This technique is a powerful tool for investigating the spatial distribution of biomolecules without the need for any time-consuming extraction, purification, and labeling procedures for biological tissue sections. The mass microscope provides clear images with regards to the distribution of hundreds of biomolecules in a single measurement, and also helps in determining the cellular profile of the biological system. In this review, we focus on some of the recent developments in clinical applications and describe how the mass microscope can be employed to assess pathomorphology and pharmacokinetics.