This paper presents the knowledge organization system developed by the French armies to manage health information. Its deployment is organized as three Information Systems. Its objective is to improve the process of creating, storing and integrating knowledge. Its mission is to help the military decision maker in managing uncertainty related to a crisis before or during a deployment. This system was tested during the chikungunya epidemic in Reunion to reduce the uncertainty of the decider before sending troops in the Island for the mosquitoes control and during the Ebola outbreak before the leaving of military experts in Guinea.