Lower respiratory disease is a major source of morbidity in military recruits, with hospitalization rates for pneumonia more than 30 times that of the non-recruit population. The etiologic agent remains unknown in over 75% of cases. This study prospectively examined the etiology of pneumonia among recruits at Naval Training Center, San Diego, California. Recruits presenting with cough, fever, or shortness of breath and pulmonary infiltrates on chest X-ray were eligible for enrollment. A standardized scoring form and focused physical exam were completed on each subject. Sputum specimens were obtained for Gram's stain and culture, DNA probing for Legionella and Mycoplasma species, and direct fluorescent antibody staining for Legionella. Acute and convalescent serologies were performed for adenovirus, influenza A and B, Mycoplasma pneumoniae, Chlamydia group, and respiratory syncytial virus. Of 110 eligible patients, 100 consented to enrollment and 75 patients completed the study. Etiologic diagnoses were obtained in 40 of the patients (53%). M. pneumoniae, Haemophilus influenzae, and viruses accounted for the majority of infections. Mixed infections were seen in six patients. Forty-seven percent of patients had no diagnosis established. Pneumonia in this series of military recruits was frequently caused by M. pneumoniae and H. influenzae. Fifty percent of cases were undiagnosed with routinely available laboratory methods. Further studies are warranted to more clearly define the etiologic agents of recruit pneumonia and the utility of prophylactic measures.