Pandemic influenza is a major challenge to emergency preparedness agencies and health systems throughout the world. It requires preparation for a situation of widespread morbidity due to flu and its complications which will lead to a huge burden on the health system in the community and in hospitals, and work absenteeism, also among health care personnel. This may require major involvement of the army in both preparedness and measures to be taken to tackle such an event. This article reviews the different roles armies could take in such a crisis, and presents the Israeli test case. Defense systems are characterized by a number of attributes that may be major advantages during pandemic influenza: crisis management capacities, ability to deal with varied tasks in sub-optimal conditions, logistic resources (fuel, food and water), widespread deployment in the country and sometimes in the world, and the ability to activate people in risky situations, even against their will. The army roles during pandemic outbreaks could include: taking national and regional command of the event, assigning workforce for essential civilian missions, use of logistic and military resources, maintaining public order and implementing public health measures such as isolation and quarantine. In addition, the army must continue its primary role of maintaining the security and guarding the borders of the state, especially in times of global geopolitical changes due to pandemic. Since March 2009, the influenza A/H1N1 2009 virus spread throughout the world, leading the WHO to declare a state of pandemic influenza. According to Israeli preparedness plans, the management of the event was supposed to pass to the defense system. However, due to the moderate severity of the illness, it was decided to leave the management of the event to the health system. In view of the necessity of maintaining military combat capabilities, and the possibility of outbreaks in combat units, which actually occurred, the Israel Defense Forces (IDF) policy for the pandemic was stricter than the policy of the Ministry of Health. Defense systems in Israel and the world should prepare, the sooner the better, for the possibility of a worse pandemic, in which the army may take a major role, especially since regular life in the country, in such a case, would be disturbed.