Systems for managing the risks associated with foodborne pathogens are based on detailed knowledge of the microorganisms and the foods with which they are associated--known hazards. An emerging pathogen, however, is an unknown hazard; therefore, to control it, key data must be acquired to convert the pathogen from an unknown to a known hazard. The types of information required are similar despite the identity of the new agent. The key to rapid control is rapid mobilization of research capabilities targeted at addressing critical knowledge gaps. In addition, longer-term research is needed to improve our ability to respond quickly to new microbial threats and help us become more proactive at anticipating and preventing emergence. The type of contingency planning used by the military in anticipating new threats serves as a useful framework for planning for new emergence.