Concern about respiratory diseases in soldiers increased in the late 1990s as production of the successful adenovirus vaccines stopped and the possibilities of an emergent pandemic influenza strain and use of bioweapons by terrorists were seriously considered. Current information on the causes and severity of influenza-like illness (ILI) was lacking. Viral agents and clinical presentations were described in a population of soldiers highly immunized for influenza. Using standard virus isolation techniques, 10 agents were identified in 164 (48.2%) of 340 soldiers hospitalized for ILI. Influenza isolates (29) and adenoviruses (98) occurred most frequently. Most influenza cases were caused by influenza A and probably resulted from a mismatch between circulating and vaccine viruses. Most (58.5%) patients with an adenovirus had a chest radiograph; 31.3% of these had an infiltrate. Clinical findings did not differentiate ILI caused by the various agents. Only 29 cases of influenza occurred in ∼7,200 person-years of observation, supporting the use of influenza vaccine.