Aim: To investigate the diagnostic value of the biochemical markers cyclophilin A (CYPA) and vascular adhesion protein-1 (VAP-1), associated with endothelial dysfunction, platelet adhesion, and arterial thrombus in pulmonary embolism (PE), in whose pathophysiology platelet activation and aggregation resulting from endothelial damage are known to be involved. Material and Method: Serum CYPA and VAP-1 levels of 165 patients presenting to the emergency department with suspected acute PE and with presence of PE investigated at spiral computerized tomography angiography were measured in this prospective clinical study. These patients were assigned into two groups, PE (+) and PE (-), based on the computerized tomography results, and their CYPA and VAP-1 levels were then compared. Results: Comparison of the two groups' measurements revealed a significant difference in terms of VAP-1 levels (p=0.0001), but none for CYPA (p=0.381). Conclusion: Diagnostic value was determined for serum VAP-1 levels in acute PE, but we couldn't detect any diagnostic value for CYPA in patients with acute PE.