Introduction: Prosthetic Valve Thrombosis (PVT) is a devastating complication of mechanical valve implantation. Treatment of PVT is usually by thrombolysis or by surgery. While the results of thrombolysis of thrombosed mitral valve is well established, results at the aortic position are not well reported. We sought to compare the results of thrombolytic therapy for thrombosed prosthetic bileaflet mechanical valve at the mitral and the aortic position. Methods: The data of 86 patients who had 94 episodes of PVT at the mitral or the aortic position, presenting between July 2001 to July 2010 at are institution were retrospectively reviewed. Results: From July 2001 to July 2010, over a period of 120 months, 4,216 patients underwent mitral valve replacement, 2,496 had aortic valve replacement, and 532 had double valve replacement using the bileaflet ATS valve. After one thrombolytic therapy course in 86 patients, there was complete resolution of hemodynamic abnormalities in 46 patients (53. 48%), partial resolution in 23 patients (26. 74%), and no change in 10 patients (19. 76%). In 9. 30% of the cases, there was a recurrence with 62. 5% full response to repeat thrombolysis. Full response to thrombolytic therapy was almost identical at both mitral and aortic position seen in about 53% of cases but whereas at mitrpartial response to thrombolytic therapy was seen in 18 patients (31%) but at aortic position only 5 patients (17%) had partial response to thrombolytic therapy. There was also a higher incidence of failure of thrombolytic therapy at aortic position, in 4 patients (28%) as against 6 patients (15%) at mitral position. Complications of thrombolytic therapy was more common with valve thrombosis at the aortic position. Conclusion: Thrombolytic therapy may be considered as first line of therapy in low risk patients. Those patients in NYHA III/IV, thrombolysis may still be used with almost 50% complete response to thrombolytic therapy and surgery can be avoided in them. Those patients who do not respond to thrombolytic therapy early should be considered for surgery especially in cases of PVT at aortic position. © 2011 Indian Association of Cardiovascular-Thoracic Surgeons.