Transmission electron microscopy is an imaging technique that visualizes the ultrastructure of samples, revealing not just the structures of interest but also the context occurring around the structures of interest. When the different approaches to transmission electron microscopy are understood and the right technique is applied to address a biological question, this imaging technique can be extremely useful for a broad diversity of samples and biological questions, including investigations into influenza A infection. In this chapter, three protocols (negative staining, chemical processing, and high-pressure freezing—freeze substitution) routinely used in the Electron Microscopy Facility at the Instituto Gulbenkian de Ciência will be presented.