Chlamydia pneumoniae is a common cause of acute and persistent respiratory tract infections. The prevalence of C. pneumoniae was studied using the polymerase chain reaction (PCR) in throat swabs from 85 consecutive children with respiratory tract infections and 86 healthy children. In retrospect, it became evident that this study was conducted in the midst of a local C. pneumoniae epidemic. 38 (45%) of the sick children and 5 (5.7%) of the healthy children were positive for C. pneumoniae by PCR. 26 of the sick children (mean age 6.4 years) were found to have otitis media either at the time of examination or shortly thereafter. Six of 9 children with acute otitis media were PCR positive for C. pneumoniae and 7 of the 9 had specific antibody responses indicating active infection. 10 of 17 children diagnosed as having otitis media with effusion were found to be positive for C. pneumoniae by PCR. Seven children had or developed persistent otitis media with effusion. Chlamydia pneumoniae was demonstrated by PCR from the middle ear fluid in 1 of the children. The results obtained from this study indicate that C. pneumoniae may be involved in the aetiology of otitis media.