Elemental analysis can be applied in the medical field to investigate the causes of disease. In patients with some pulmonary diseases, elements can be found in the exogenous dust deposited in the lungs and are also accumulated through the loss of cell homeostasis. Diseases induced by inhalation of dust typically affect the lungs. Although there are many pulmonary diseases induced by dust inhalation, it is often difficult to clarify the exact cause. In-air microparticle induced X-ray emission (in-air micro-PIXE) analysis is a method of elemental analysis that employs a proton ion-beam to directly measure the content of elements and their distribution in frozen sections or paraffin sections of tissue. We constantly inhale particles while breathing, but most of us do not develop pulmonary disease. Because in-air micro-PIXE analysis can determine the two-dimensional localization and content of particles in tissue, we can clarify the relationship between inhaled particles and diseases based on such analysis and the immunohistochemical expression of disease-related proteins. Elemental analysis methods like in-air micro-PIXE analysis may be useful for making precise diagnosis amd assesing disease progression to overcome threat such as occupational or environmental exposure.