Midshipmen at the U.S. Naval Academy have recently suffered epidemics of upper respiratory tract infections. Seeking to determine cause, in June 1998 we enrolled 1,243 (99.5%) of 1,249 new midshipmen (plebes) and followed them during their first 11 months of training. Eighty-five plebes sought medical attention for acute respiratory disease. Using culture, serologic studies, and polymerase chain reaction, considerable evidence for respiratory pathogen infection was found among the ill subjects: Chlamydia pneumoniae in 41 (52.6%), Mycoplasma pneumoniae in 19 (25.3%), influenza in 11 (14.2%), Streptococcus pneumoniae in 6 (7.3%), and adenovirus in 1 (1.2%). Additionally, 873 (81%) the 1,077 plebes who completed an end-of-year questionnaire complained of having one or more respiratory symptoms (> 12 hours) during their first year of school. Of these, 132 (15%) reported that the symptoms significantly affected their performance. Study results suggest that respiratory infections were frequent, had a significant adverse impact on training, and were often attributable to bacterial pathogens.