Cereal-based foods are derived from grains that have a well-organized microstructure. The cell wall thickness, size of cells, starch granule structure, protein structure and distribution, the amount and size of fat droplets and their distribution etc. vary in the kernels of the various cereals and in many cases between varieties. Processing, such as milling, dough mixing and baking, causes microstructural changes in cell and tissue structures, proteins, cell wall components, starch and fat droplets. The microstructure determines the appearance, texture, taste perception and stability of the final product. A variety of microscopic techniques is available for studying the microstructure of cereals. In research on cereal-based products fluorescence microscopy provides resolution, chemical specificity, and sensitivity rarely matched by other techniques. As an addition to chemical analysis microscopy helps to understand and visualize structural changes and textural differences in cereal grains, food and feed. The aim of this paper is to give an overview of the possibilities of light microscopy in cereal research.