This chapter introduces the reader to the treatment of infections with antimicrobial drugs. In doing so, an ecological and evolutionary approach is taken that sees humans as just one part of the biosphere, which is the totality of life on earth. Our interaction with microorganisms is constant and ever changing, and it is this dynamic relationship between evolving organisms that makes the treatment of infectious diseases so challenging. Early in this chapter, this ecological approach is introduced, followed by the key to treating infectious diseases, which is the concept of selective toxicity. After that the key groups of organisms and their treatment are discussed, most notably bacteria, viruses, and fungi, but also protozoa and helminths. More general topics of identification, testing, and resistance are then discussed and this chapter concludes with the consideration of opportunistic infections and pharmacological approaches to prevention.