When charged particles collide with atoms, atomic inner shell electrons become ionized, producing characteristic X-rays. This phenomenon is called particle-induced X-ray emission (PIXE). The characteristic X-ray production cross-sections from PIXE are very large, and the characteristic X-rays of elements contained in a sample are easily measured by a Silicon detector with a high energy resolution. Hence, sodium to uranium can be detected with a sensitivity of ppb~ppm, and PIXE has been applied to trace element analysis. Scanning ion beams can be used to obtain the spatial distributions of elements in a sample. Furthermore, the distributions of elements inside a cell can be investigated using micro ion beams. PIXE analysis is a very useful technique for multi-elemental analysis and is now widely used in many fields and applications, including chemistry, medicine, biology, archaeology, agriculture, materials science, fisheries science, geology, petrology, environmental study, contamination monitoring, resource search, semiconductors, metal, astrophysics, earth science, criminal investigations, and food.