The aim of this study was to conduct an epidemiological and laboratory surveillance of Influenza-Like Illnesses (ILI) in Polish Armed Forces, civilian military personnel and their families in 2011/2012 epidemic season, under the United States Department of Defense-Global Emerging Infections Surveillance and Response System (DoD-GEIS). ILI incidence data were analyzed in relation to age, gender, patient category as well as pathogen patterns. Multiple viral, bacterial and viral-bacterial co-infections were identified. Nose and throat swabs of active duty soldiers in the homeland country and in the NATO peacekeeping forces KFOR (Kosovo Force), as well as members of their families were tested for the presence of viral and bacterial pathogens. From October 2011 to May 2012, 416 specimens from ILI symptoms patients were collected and analyzed for the presence of viral and bacterial pathogens. Among viruses, coronavirus was the most commonly detected. In the case of bacterial infections, the most common pathogen was Staphylococcus aureus.