Of the analytical electron microscopy techniques available, electron probe X-ray microanalysis has been most widely used for the study of biological specimens. This technique is able to identify, localize, and quantify elements both at the whole cell and at the intracellular level. The use SEM or TEM to analyze individual whole cells gives a simple and rapid method to study changes in ion transport after stimulation, whereas the analysis of thin sections of cryoprepared cell sections, although technically more difficult, allows details about ionic content in intracellular compartments, such as mitochondria, ER, and lysosomes, to be obtained. In this chapter the principles underlying X-ray emission are briefly outlined, step-by-step methods for specimen preparation of whole cells and cell sections for microanalysis are given, as are the methods used for deriving quantitative information from spectra. Areas where problems might occur have been highlighted. The different areas in which X-ray microanalysis is being used in the study of cell physiology are briefly reviewed.