Infectious diseases are a leading cause of human morbidity and mortality worldwide, and they are caused by a variety of pathogenic bacteria, viruses, parasites, and fungi. The interactions between pathogen and host require rapid adaptation and evolution to avoid death, from the perspective of both the host and the pathogen. Epigenetic processes in both the host and pathogen are the key to the outcome of these interactions. This chapter provides an overview and examples of host epigenetic responses to pathogens via histone modifications, DNA methylation, chromatin-associated complexes, and noncoding RNAs. Survival of pathogens in the human host depends on appropriate adaptation to distinct microenvironments within the host and differences between individual hosts. In both cases, the invading pathogen is challenged by the dynamic processes of the host’s innate and adaptive immune responses. In recent years, the importance of the role of epigenetic regulation in pathogens has been appreciated and is reviewed in this chapter, with a particular focus on the epigenetics of human bacterial pathogens.