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Objectives Dabigatran is a direct thrombin inhibitor shown to be an effective alternative to warfarin in patients with non-valvular atrial fibrillation (AF). We evaluated the use of dabigatran in patients with bioprosthetic mitral and/or aortic valve replacement and AF. Methods We selected 34 and randomized 27 patients in a 1:1 ratio to receive dabigatran or warfarin. The primary endpoint was the presence of a new intracardiac thrombus at 90 days, by transesophageal echocardiogram (TEE). Secondary endpoints included the development of dense spontaneous echo contrast (SEC) and incidence of stroke (ischemic or hemorrhagic), myocardium infarction, valve thrombosis and peripheral embolic events. Results The trial was terminated prematurely because of low enrollment. There were 27 patients in total: 15 patients placed in the dabigatran group and 12 in the warfarin group. After 90 days, one patient (8.3 %) in the warfarin group and none in the dabigatran group had developed a new intracardiac thrombus. In the dabigatran group, two patients (13.3 %) developed dense SEC versus one patient (8.3 %) in the warfarin group. In the warfarin group, one patient (8.3 %) presented ischemic stroke, and none did in the dabigatran group. We observed no cases of hemorrhagic stroke, valve thrombosis, embolic events or myocardial infarction in either group throughout the study. However, one patient (6.7 %) in the dabigatran group had a fully recovered transient ischemic attack and one patient in the warfarin group died of heart failure. Conclusions The use of dabigatran appears to be similar to warfarin in preventing the formation of intracardiac thrombus. Trial Registration Clinicaltrials.gov NCT01868243.