The Bundeswehr Institute of Microbiology is a governmental research facility that specialises in medical biodefence. It is tasked with the development of procedures and measures to protect Bundeswehr personnel from conditions caused by biothreat agents and to restore their health in case of illness. The Institute therefore applies scientific methods to deal with a multitude of pathogens and biological toxins that could potentially be misused as biological weapons. These are pathogens or toxins which rarely occur in nature and as a rule cause severe, sometimes fatal diseases that can easily be transmitted from person to person and/or are difficult to treat. One of the aims of our research is the ability to identify these pathogens unambiguously. The test methods set up in this context also serve to investigate obscure outbreaks of diseases in order to assess whether the pathogen involved could have been deliberately released. As a matter of course, this also involves diagnostic differentiation from common infectious diseases. The diagnostic capabilities resulting from this mission also offer a multitude of possible applications in the diagnosis of natural infections and outbreaks which may be caused by the same pathogens.