Mycoplasma pneumoniae, Legionella pneumophila and Chlamydia pneumoniae are the most common bacterial agents, which account for 15-40%, 2-15% and 5-10% of atypical community-acquired pneumonia (CAP) respectively. These agents are mostly associated with infection in the outpatient setting. The aim of this study was to evaluate the frequency of these pathogens among patients with CAP attending outpatient clinics in Tehran. A cross-sectional study was carried out of 150 patients attending to educational hospitals in Tehran with CAP. M. pneumoniae, L. pneumophila and Chlamydia spp. were detected by PCR assay, targeting the P1 adhesion gene, macrophage infectivity potentiator (mip) gene and 16S rRNA gene respectively from throat swabs obtained from each patient. A total of 86 (57.3%) of 150 patients were women; median age was 50 years (interquartile range, 35-65 years). M. pneumoniae, L. pneumophila and Chlamydia spp. were detected in 37 (24.7%), 25 (16.7%) and 11 (7.3%) patients respectively; of these, 66 patients (44%) were infected at least by one of these three pathogens. The frequency of L. pneumophila was significantly higher among patients over 60 years old (p 0.03). Coinfection was detected in seven patients (4.7%); six were infected by M. pneumoniae and L. pneumophila, and only one was infected by L. pneumophila and Chlamydia spp. M. pneumoniae was the most prevalent agent of atypical CAP, and L. pneumophila was more likely to infect elderly rather than younger people. Further studies on the prevalence of CAP and its aetiologic agents are needed to improve the diagnosis and treatment of CAP patients.