This chapter describes some microscopical approaches for analyzing the structure of endomycorrhizal infections, identifying modifications in protein expression (enzyme activities) and localizing specific molecules at both the tissue and cellular level. Techniques are chosen to illustrate how they can not only increase the understanding of how endomycorrhizal symbionts interact with each other, but also furnish potential tools for diagnosing the functional state of the symbiosis. Non-destructive observations can be made of vesicular-arbuscular endomycorrhizal infections in root pieces using ultraviolet light. Although this can be useful for selecting materials for biochemical analysis or electron microscope preparation, the technique is limited to young root tissues in which only living arbuscules can usually be detected. The chapter illustrates cytological, histochemical, and immunocytochemical techniques. It provides powerful tools for studying the structure and function of symbionts and their interactions in endomycorrhiza. Knowledge of the physical and chemical nature of cellular and subcellular structures permitting functional compatability in endomycorrhizal associations has been considerably improved and subcellular localization of enzyme activities has given some insight into their physiological significance for the symbiotic condition. Furthermore, by combining immunolocalization with ultra cytoenzymology it is possible to understand how the synthesis and the expression of the molecules involved are regulated.