Chlamydia pneumoniae is a recently reported, but common, respiratory tract pathogen. The organism has been detected by electron microscopy, immunocytochemistry, polymerase chain reaction (PCR) and recently culture within atherosclerotic plaques, suggesting a possible association between C. pneumoniae infection and atherosclerosis. Interestingly this association has not been found by all researchers. We examined 17 carotid endarterectomy specimens, 16 carotid arteries and 16 coronary arteries from autopsy specimens. They were examined by PCR for the presence of C. pneumoniae. In none of the 49 atherosclerotic samples examined was C. pneumoniae detected. The sensitivity of our PCR assay was rigorously tested and found to detect consistently fewer than ten elementary bodies. The association between C. pneumoniae and atherosclerosis is intriguing but has not yet been demonstrated in Australian patients.