Atrial fibrillation (AF) is a risk factor for cerebral embolism, with the left atrial appendage (LAA) being considered as the source of emboli. However, the relationship between the histologic properties of LAA thrombi and the occurrence of cerebral embolism is not known. Seventy-six hearts from patients who died within 1 month after cerebral embolism were studied at autopsy. Patients were grouped according to the presence of AF and the presence of valvular disease (VD). We determined whether the LAA thrombi adhered to the trabecular region or the remainder of the LAA. LAA thrombi were grouped into three stages: a fresh stage in which thrombi consisted of fibrin and platelets, an organizing stage in which angiogenesis was observed in the thrombi, and an organized stage in which endothelial cells covered the surface of the thrombi. The AF+/VD– group included 19 patients (25.0%), the AF+/VD+ group 8 (10.5%), the AF–/ VD– group 37 (48.7%), and the AF–/VD+ group included 12 patients (15.8%). LAA thrombi were observed in 15 patients (78.9%) in the AF+/VD– group, and all of the thrombi adhered to the trabecular region. Thrombi in the fresh and the organizing stages were observed in 10 patients (66.7%). Patients in the AF+/VD– group accounted for about 25% of the cases of cerebral embolism. All of these thrombi were attached to the trabecular region, and about 70% of them could represent an embolic source.