Nasopharyngeal and throat swabs taken from 66 patients presenting at the Department of Infectious Disease with symptoms of upper and lower respiratory tract infection were analysed by use of the polymerase chain reaction (PCR) for Chlamydia pneumoniae and Mycoplasma pneumoniae. A total of 18 patients (27%) were positive by PCR for C. pneumoniae. All 18 patients were positive from throat swabs, and three were also positive from nasopharyngeal specimens. The difference between the outcome of PCR using throat and nasopharyngeal swabs was statistically significant. A total of 7 patients (10.6%) were positive for M. pneumoniae and of these, 6 were positive from throat swabs and 2 were positive from nasopharyngeal swabs. This difference was not statistically significant, probably due to the low numbers of positive patient specimens.