This chapter discusses applications of X-ray microanalysis to plant and fungal tissues with emphasis upon plant-disease associations. Since the early 1960s, X-ray microanalysis has provided a method of elemental analysis at the microscopic level and has been used at the subcellular level to determine the location of major inorganic ions for both plant and animal systems. There are many types of equipment which can be used for X-ray microanalysis of biological samples. These instruments include the following: X-ray fluorescence, electron microprobe or "probe", scanning electron microscope, transmission electron microscope, and scanning transmission electron microscope. Freeze substitution with dry thin sections and X-ray microanalysis were used to demonstrate that sodium and chloride concentrations increased with salinity in the cytoplasm, vacuole, and cell wall of the marine fungus Dendryphiella, although potassium concentrations decreased with salinity. The concern with aluminum toxicity and localization and mineral element distribution in Norway spruce roots led to studies with X-ray microanalysis.