Introduction Mycoplasma pneumoniae is a major cause of atypical community-acquired pneumonia) CAP) with a prevalence range of 15-20% and up to 40% in adults and children, respectively. In Iran, the recorded frequency ranges between 1-6.15%. We aimed to investigate the frequency of M. pneumoniae among patients with atypical pneumonia acquired from the community. Methods Over a period of 5 months between January and June 2017, 520 patients with suspected CAP, who had been to the hospital outpatient clinics of Tehran University, were enrolled in this study. Throat swab specimens were obtained from 110 outpatients who presented with symptoms of atypical pneumonia. M. pneumoniae was identified via culture and biochemical tests, such as fermentation of glucose and arginine, hemolysis, and hemadsorption. For confirmation, PCR was performed to amplify the gene fragment coding for p1 adhesin. Results The major and minor clinical signs of the patients were dyspnea (67.3%) and nausea (15.5%), respectively. Out of 110 specimens, 25 (22.7%) and 29 (26.4%) isolates were identified to be M. pneumoniae via culture and molecular assay, respectively. Comparing the results of the two methods, the PCR showed better sensitivity and rapidity for the detection of M. pneumoniae. There was a high congruence between culture and the PCR assay; kappa level was 'almost perfect' (κ=0.90). Conclusion This is the first report of high frequency of M. pneumoniae in our region. This finding can serve as baseline information for further investigation and confirmation of the potential epidemics of M. pneumoniae pneumonia in our community.