The Department for Infectious Disease Epidemiology of the Robert Koch Institute (RKI), German national public health institute, is in charge of national surveillance, prevention, control strategies and epidemiological research in the field of infectious diseases. Together with external senior experts the Department initiated a prioritization process aiming to (1) develop a rational system for setting priorities in the area of infectious diseases using a metric-consensus approach, and (2) rank most common pathogens in accordance with their importance for national surveillance and epidemiological research to guide future work of the RKI.