During endemic infections, the sensitivity of diagnostic tests and rapid diagnosis of the respiratory tract pathogens is particularly important. Utilization of just one diagnostic technique, such as serological tests or polymerase chain reaction (PCR)-based detection methods, during outbreaks of lower respiratory tract infections (LRI) can result in some of the patients being missed. In this study we aimed to investigate the etiology of LRI in military recruits in Izmir, Turkey, among whom several pneumonia cases have been reported and 47 patients have been hospitalized. Nasopharyngeal swabs were used for PCR analysis of Chlamydophila pneumoniae, Mycoplasma pneumoniae and Legionella spp. Serum samples were collected in the acute and convalescent phase of infection for C. pneumoniae and M. pneumoniae. Thirty-nine patients were diagnosed with C. pneumoniae infection by PCR and/or serology. Diagnoses were established by PCR in the acute phase of infection in 40.4% of the group. Based on the results of these studies, PCR is a useful method for early detection and identification of C. pneumoniae-related LRI outbreaks. However, this technique is not sufficient to detect all positive cases per se. After effective therapy and introduction of appropriate infection control measures, the outbreak ceased without mortality. This is the first closed-community C. pneumoniae outbreak report from Turkey.