In October 1998, Hurricane Mitch claimed several thousand lives and left hundreds of thousands of people homeless in Central America. Numerous agricultural resources and infrastructure were destroyed. On November 1, France deployed a major humanitarian aid operation. For the first time, epidemiologists from the National Public Health Network accompanied the French relief teams, Civil Security, and Samu Mondial. The epidemiologists’ objectives were: to rapidly assess epidemic risks; to provide epidemiological support to the French contingent; to provide methodological support to local health authorities for investigating epidemics and establishing appropriate surveillance systems to describe the cholera epidemic raging in Guatemala and evaluate its management; to assess and prevent health risks due to the environmental release of drums containing phytosanitary products in Honduras and to manage a leptospirosis outbreak in Nicaragua. This experience demonstrated the value of integrating epidemiological tools into a humanitarian aid framework. However, implementing the epidemiological approach from the exploratory phase onward allowed for a better alignment of the program’s objectives and resources with health needs. For this reason, it is recommended that an epidemiological dimension be integrated into the planning of humanitarian aid that France is likely to mobilize during such events.