In April 2009, the World Health Organization announced the emergence of a novel influenza A(H1N1-09) virus and in June 2009 declared the outbreak a pandemic. The value of military structures in responding to pandemic influenza has become widely acknowledged in recent years. In 2005, the Israeli Government appointed the Ministry of Defense to be in charge of national preparedness and response for a severe pandemic influenza scenario. The Israeli case offers a unique example of civilian-defense partnership where the interface between the governmental, military and civilian spheres has formed a distinctive structure. The Israeli pandemic preparedness protocols represent an example of a collaboration in which aspects of an inherently medical problem can be managed by the defense sector. Although distinctive concepts of the model are not applicable to all countries, it offers a unique forum for governments and international agencies to evaluate this interface within the context of pandemic influenza.