A serological study was undertaken to investigate infections in active-duty United States soldiers with illnesses characterized by prolonged, afebrile, nonproductive coughs. Fifty-four soldiers were enrolled with such illness of >/=2 weeks' duration (case patients) along with 55 well soldiers (control subjects). Serum samples were tested for IgG and IgA antibody to 3 Bordetella pertussis antigens, pertussis agglutinins, IgM antibodies to Mycoplasma pneumoniae, IgM and IgG antibodies to Chlamydia pneumoniae, and IgM antibody to adenoviruses. Forty-six case patients (85%) had evidence of recent infection with Bordetella species, M. pneumoniae, or C. pneumoniae, and many had evidence of mixed infections; there were 27 Bordetella species, 20 C. pneumoniae, and 33 M. pneumoniae recent infections. Fifteen case patients had high titers of IgG or IgA to B. pertussis filamentous hemagglutinin without high titers of antibodies to other B. pertussis antigens, which suggested the presence of cross-reacting antibodies to M. pneumoniae and perhaps C. pneumoniae or unidentified infectious agent or agents. Since illnesses due to Bordetella species, M. pneumoniae, and C. pneumoniae can all be treated with macrolide antibiotics and B. pertussis illness can be prevented by immunization, and since military readiness was affected in 63% of the cases, it seems important to conduct further studies in military populations.