Background - The aim of this study was to investigate the presence of various atypical pneumonia agents (Chlamydia pneumoniae, cytomegalovirus, Mycoplasma pneumoniae), which are considered to have a role in the ethiopathogenesis of atherosclerosis, in aortic biopsies without macroscopically visible plaque and in internal thoracic artery biopsies. Material and methods - Thirty-three patients (group 1), who had undergone coronary bypass operation and 10 non-atherosclerotic patients (group 2), were included in the study. Seventy-six tissue biopsies were taken. Biopsies from the patients in group I a were obtained from the atheroma plaque-free aortic tissue-and 33 biopsies (group 1b) were obtained from their internal thoracic arteries. Following DNA extraction, nested PCR was used to detect Chlamydia pneumoniae DNA, and real time PCR was used to detect cytomegalovirus and Mycoplasma pneumoniae DNA. Blood parameters (lipid profile, CRP, fibrinogen) of the patients and operation characteristics were recorded. Results - Chlamydia pneumoniae DNA was detected in 5 of 33 biopsy samples from coronary bypass patients, whereas none of the control patients (group 1b and group 2) were positive for this agent (P = 0.001). Neither CMV nor Mycoplasma pneumoniae was detected in IMA and aortic biopsies of both bypass and control patients. Elevated total cholesterol levels (P = 0.02) and positive CRP (P = 0.001) was found in C. pneumoniae positive patients. Prevalence of acute coronary syndrome was significantly higher in C. pneumoniae detected patients compared (P = 0.001). Conclusions - Detection of C. pneumoniae DNA in the atheroma free aortic biopsies might indicate that this micro-organism intervened in the progression of atheroma plaque. There was a strong relationship between the detection of this micro-organism in the aortic wall and acute coronary syndrome. The absence of DNA of the corresponding micro-organisms in the IMA wall may show its resistance to infective agents and in turn to atherosclerosis, which is a result of the prevailing endothelial functions of this artery.