Objectives This study sought to identify risk factors for thrombus formation on the Amplatzer Cardiac Plug (ACP) (St. Jude Medical, St. Paul, Minnesota) after left atrial appendage occlusion. Background Left atrial appendage occlusion with the ACP aims to reduce the risk of embolic stroke and bleeding complications associated with vitamin K antagonists in patients with atrial fibrillation. Methods We performed transesophageal echocardiography before discharge and after 3, 6, and 12 months in 34 patients with atrial fibrillation undergoing ACP implantation and receiving dual antiplatelet therapy. Clinical, echocardiographic, and hemostaseological parameters were retrospectively analyzed to identify risk factors for thrombus formation. Results Three patients had thrombi before discharge, 3 more at the 3-month follow-up. No differences were found in left atrial volume, left atrial appendage velocity, spontaneous echo contrast, transmitral gradient, or mitral regurgitation between patients without or with thrombi. CHADS2 (Congestion, Hypertension, Age, Diabetes, and Stroke) score (2.0 ± 1.1 vs. 4.3 ± 1.0), CHA2 DS2 -VASc (CHADS2 plus Vascular Disease and Sex Category) score (5.2 ± 1.3 vs. 6.8 ± 0.8), and pre-interventional platelet count (215.9 ± 63.9/nl vs. 282.5 ± 84.4/nl) were higher and ejection fraction (50.6 ± 11.4% vs. 39.7 ± 10.6%) lower in those with thrombi. Factor 2, factor 5, or methylenetetrahydrofolate reductase mutations and genetic variants associated with reduced clopidogrel activity were not more frequent in patients with thrombi. Conclusions Transesophageal echocardiography identified 17.6% of patients with thrombus formation on the ACP despite dual antiplatelet therapy. CHADS2 and CHA2 DS2 -VASc scores, platelet count, and ejection fraction are risk factors for such thrombus formation.