Background The role of Chlamydia pneumoniae in the pathogenesis of aortic aneurysm is controversial. We investigated the presence of C. pneumoniae in tissue samples excised from patients and controls. Methods Aortic wall specimens were obtained from 17 patients with acute Stanford type A aortic dissection, 25 patients with thoracic aortic aneurysms (TAA) and 23 patients with abdominal aortic aneurysms (AAA). Eighty-three tissue samples of 73 control patients free of aortic disease were obtained either at surgery or autopsy. The presence of Chlamydia subspecies DNA (sequences specific for all known Chlamydiaceae) and DNA of C. pneumoniae, C. trachomatis and C. psittaci were assessed by a validated highly sensitive and specific real time polymerase chain reaction (PCR) analysis. Atherosclerotic risk factors were assessed in all patients. Results We failed to detect C. pneumoniae and C. psittaci-DNA in any of the 148 vessel specimens. C. trachomatis-DNA was detected in 1/65 patients and in none of 83 controls ( P=0.43). Chlamydia subspecies DNA was found in samples of eight cases and in one control ( P=0.01), however, no significant differences were found between the subgroups aortic dissection ( P=0.09), TAA ( P=0.99) and AAA ( P=0.15) and respective controls. Conclusions C. pneumoniae does not play a clinically relevant role in acute and chronic aortic disease. The impact of other organisms of the family Chlamydiaceae needs further evaluation.