This study examined the prevalence of atypical pathogens causing community-acquired pneumonia (CAP) in Korea. We collected sera and clinical data for a period of 1 year for the adult patients consecutively admitted to Chunchon Sacred Heart Hospital with CAP. The diagnosis was made using serologic methods to detect antibodies for Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella spp., Chlamydia psittaci, and Coxiella burnetii. Among 81 recruited patients, C. pneumoniae (n = 10, 12.3%) was the leading cause of illness, followed by M. pneumoniae (n = 7, 8.6%). One case of C. burnetii pneumonia was detected, but there were no cases of Legionella spp. or C. psittaci. Three cases of C. pneumoniae pneumonia were co-infected with either M. pneumoniae or C. burnetii. There was no significant difference between atypical pneumonia and non-diagnosed pneumonia in terms of clinical manifestations. In conclusion, of the atypical pathogens causing CAP, C. pneumoniae and M. pneumoniae appear to be the important etiologic pathogens in Korea.