Rationale and Objectives: The detection of pulmonary embolism is still challenging due to the often non-specific clinical findings. The aim of this study was to investigate the potential of molecular targeted MR-imaging of pulmonary emboli using low dose application of a fibrin-specific contrast agent (EP-2104R, EPIX Pharmaceuticals, Cambridge, MA, USA). Methods: Fresh clots from human blood were engineered ex-vivo and delivered in the lungs of eleven swine. Subsequently, a T1-weighted breath-hold 3D gradient-echo sequence was performed before as well as 5 minutes, 1 hour and 2 hours after systemic administration of 7.5(n=5) or 4(n=5) µmol/kg EP-2104R. One swine that did not receive any contrast agent served as a control. MR images were analyzed by two investigators and contrast-to-noise ratio (CNR) between the thrombus and the surrounding tissue (blood-pool and lung parenchyma) was assessed. Localization of thrombi was compared to 16-row multi-slice CT. Finally, the animals were sacrificed and thrombi were removed for assessment of Gadolinium concentration. Main Results: Prior to contrast media application thrombi were not visible on MR-images. One and 2 hours after contrast media injection pulmonary emboli were selectively visualized with high signal intensity foci, independent of the dosage used. A high Gadolinium concentration in thrombi was found after both dosages (83 ± 41 µM for 4 µmol/kg and 130 ± 57 µM for 7.5 µmol/kg) resulting in a similar high CNR on MR images (between 11 and 13). Conclusion: Systemic low dose application of EP-2104R allows for selective molecular MR-imaging of fresh pulmonary thrombembolism in a swine model.