Earlier studies have associated atherosclerosis with Chlamydia pneumoniae infection. C. pneumoniae may circulate via monocytes and migrate into plaques by leukocyte infiltration; however, detection is difficult. We developed a novel polymerase chain reaction (PCR) method to test the hypothesis that C. pneumoniae DNA in circulating leukocytes is correlated with C. pneumoniae DNA in plaque material and that C. pneumoniae copy number is associated with disease severity. We obtained plaques from 130 patients who underwent surgery for carotid stenosis, aneurysm, or peripheral vascular disease. From 60 patients and 51 normal control subjects we also obtained circulating leukocytes. The C. pneumoniae 16 S rRNA gene was amplified with a highly specific quantitative PCR protocol relying on the TaqMan technology. Immunohistochemistry was performed with antibody against the C. pneumoniae outer membrane protein. C. pneumoniae DNA was present in 25% of atherosclerotic plaques and 20% of circulating leukocytes from patients. The copy number was not correlated with disease severity. C. pneumoniae DNA was more common in younger patients and smokers. C. pneumoniae antibody titers, C-reactive protein, fibrinogen, leukocyte count, cholesterol, and diabetes were not associated with C. pneumoniae DNA. Although immunostaining of plaque and PCR results were highly correlated, we found no relationship between C. pneumoniae DNA in plaques and that in circulating leukocytes. Finally, 13% of normal control subjects had positive leukocytes; however, their copy number was significantly lower than that of the patients. C. pneumoniae DNA is frequent in atherosclerotic plaques and is correlated with positive immunohistochemistry. C. pneumoniae DNA may also be found in circulating leukocytes; however, infected leukocytes and plaques do not coincide. Serology is unreliable in predicting C. pneumoniae DNA. Smoking increases the risk of harboring C. pneumoniae DNA. Our results do not suggest that either test for antibodies or C. pneumoniae DNA from leukocytes in blood is of value in predicting infected plaques.