The three-dimensional (3D) structures of the right atrial appendage (RAA) and left atrial appendage (LAA) were compared to clarify why thrombus formation less frequently occurs in RAA than in LAA. Morphological differences between RAA and LAA of 34 formalin-preserved cadaver hearts were investigated. Molds of RAA and LAA specimens were made and the neck areas, volumes of the atrial appendages (AA), and amount of pectinate muscles (PMs) were analyzed using multidetector computed tomography. In RAA, most PMs were connected to one another and formed a "dendritic" appearance and the inner surface area was smaller than in LAA. RAA had smaller volumes and larger neck areas than LAA. The ratios of the neck area/volume were larger and the amounts of PMs were smaller in RAA than in LAA. The volumes, neck areas, and amount of PMs of RAA were significantly correlated with those of LAA. According to the 3D structure, RAA appears to be suited for a more favorable blood flow, which may explain why the thrombus formation is less common in RAA than in LAA. Examining not only LAA but also RAA by transesophageal echocardiography may be useful in high-risk patients of thrombus formation in LAA because the volume, neck area, and amount of PMs of LAA reflect the shape of RAA.