The organization of the response to infectious disease outbreaks by public health agencies at the federal, state, and local levels has historically been based on traditional public health functions (e.g., epidemiology, surveillance, laboratory, infection control, and health communications). Federal guidance has established a framework for the management of domestic incidents, including public health emergencies. Therefore, public health agencies have had to find a way to incorporate traditional public health functions into the common response framework of the National Incident Management System. One solution is the development of a Science Section, containing public health functions, that is equivalent to the traditional incident command system sections. Public health agencies experiencing difficulties in developing incident management systems should consider the feasibility and suitability of creating a Science Section to allow a more seamless and effective coordination of a public health response, while remaining consistent with current federal guidance.