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Pathogens have evolved a wide variety of strategies to circumvent the host microbicidal activities and to use the cellular machinery to their own advantage. This chapter is devoted to electron microscopy, which is the approach of choice for optimal resolution and precision. A wide variety of cytochemical and immunoelectron microscopy methods can be used to characterize pathogens, analyze the intracellular compartment in which they reside, and localize bacterial virulence factors or cell components involved in their survival. Some of the major morphological methods, recent and less recent, of special interest to host-pathogen interplay are reviewed in this chapter. Phagosomes that retain intermingling characteristics of early endosomes are considered to be immature; those that become mature lose their ability to fuse with early endosomes and fuse with lysosomes to become phagolysosomes. Endocytosis and phagocytosis both involve an extensive transfer of membrane in both directions between the cell surface and intracellular membrane compartments. Given the large amounts of membrane required during uptake of particles and also during replication of endoparasites within their phagocytic vacuole, one of the questions that have been raised recently was whether other cell compartments, and more especially the endoplasmic reticulum (ER), could be an additional source of membrane for forming and/or dividing phagosomes.