Objective: The aim of this study was to investigate whether bacterial and viral infectious agents can be demonstrated in atherosclerotic lesions of patients with coronary artery disease (CAD) as well as in stenotic aortic and mitral valves from patients undergoing heart valve replacement. Methods: In this cross-sectional study, the presence of Chlamydophila pneumoniae, Mycoplasma pneumoniae, Cytomegalovirus (CMV), and Epstein-Barr virus (EBV) was investigated by polymerase chain reaction in atherosclerotic and non-atherosclerotic vascular samples taken from patients undergoing coronary artery bypass surgery due to CAD, and from patients undergoing aortic (AVR) and/or mitral valve replacement (MVR) secondary to valvular stenosis. For statistical analyses ANOVA, Chi-square test or Fisher’s exact test were used. Results: The presence of C. pneumoniae, M. pneumoniae, and CMV in atherosclerotic versus non-atherosclerotic samples was as follows: 30% vs. 16.7% (p=0.222), 6.7% vs. 3.3% (p=0.554), and 10% vs. 0% (p=0.076), respectively. In valve group, same pathogens were present in AVR and MVR patients as follows: 24.2% vs. 21.4% (p=0.773), 9.1% vs. 7.1% (p=0.758), and 21.2% vs. 11.9% (p=0.275). EBV DNA was not detected in any of vascular specimens, but in one (3%) patient with AVR (p=0.256). Conclusion: Our results suggest that C. pneumoniae, M. pneumoniae, and CMV are present with similar frequency both in atherosclerotic and non-atherosclerotic vessels. We conclude that although non-atherosclerotic, vascular samples of CAD patients are invaded by infectious agents as like as atherosclerotic vessels. We further conclude that C. pneumoniae, M. pneumoniae, and CMV are present in stenotic aortic and mitral valves and atherosclerotic tissues with similar frequency indicating that atherosclerosis and valvular stenosis might share a common etiology related to infection.