Diagnostic medical bacteriology consists of two main components: identification and typing. Molecular biology has the potential to revolutionize the way in which diagnostic tests are delivered in order to optimize the care of infected patients, whether they are in hospital or in the community. Since the discovery of the polymerase chain reaction (PCR) in the late 1980s, an enormous amount of research has enabled the introduction of molecular tests into several areas of routine clinical microbiology. Molecular biology techniques continue to evolve rapidly, and many laboratories have been reluctant to introduce these new methods due to concerns that the technology would become outdated. In consequence, the vast majority of clinical bacteriology laboratories do not currently use any molecular diagnostics, although such technology is becoming more widespread in specialized regional laboratories, as well as in national reference laboratories. Presently, molecular biology offers a wide repertoire of techniques and permutations. This chapter is intended to explore the application of these in the diagnostic laboratory setting.