In this study the aetiology of community-acquired pneumonia (CAP) in Japan was investigated and the incidence of causative pathogens in ambulatory and hospitalized patients was compared. In addition, the roles of Chlamydophila felis and Chlamydophila pecorum as causes of CAP were investigated. Five hundred and six patients with CAP who visited an outpatient clinic or were admitted to one of three different hospitals were enrolled in this study; 106 of them were outpatients and 400 were hospitalized patients. Among the 506 CAP cases, Mycoplasma pneumoniae was the most common pathogen found in the outpatients and Streptococcus pneumoniae was the most common in the hospitalized patients. No cases of Chlamydophila pecorum pneumonia were observed and only one patient had an antibody titre suggestive of recent infection with the feline strain of Chlamydophila. The incidence of infection with M. pneumoniae and Chlamydophila pneumoniae was higher among the outpatients than among hospitalized patients, whereas the incidence of infection with S. pneumoniae and Haemophilus influenzae was higher among the hospitalized patients. Recognition of these results will allow prompt and appropriate antimicrobial therapy to be provided using Japanese CAP guidelines.