The left atrial appendage (LAA) is a major source of emboli responsible for cardioembolic stroke (CES). We hypothesized that there could be differences in the morphologic and functional features of LAAs among patients with atrial fibrillation (AF) alone, patients with cardioembolic transient ischemic attack (CETIA), and patients with CES. Patients with AF and CETIA/CES were included in either a CETIA group or a CES group. Patients with AF without past histories of stroke were included in an AF/non-CVA (cerebrovascular accident) group. Cardiac computerized tomography and transesophageal echocardiography were employed for morphologic and functional assessments of LAAs. Cauliflower LAA morphology increased and chicken wing LAA morphology decreased in frequency in the following order: AF/non-CVA, CETIA, and CES group. LAA orifice diameters were larger in the CETIA and CES groups than in the AF/non-CVA group. LAA flow velocity was higher in the CES group than in the other groups. Multiple multinominal regression analyses showed that the cauliflower morphology was associated with CETIA and CES; however, after LAA orifice diameters and flow velocity were adjusted, LAA morphology was associated with neither of them. Receiver operating characteristic curve analysis showed that LAA orifice diameter and flow velocity accurately predicted CETIA (c-statistic 0.839) and CES (c-statistic 0.896), respectively. In conclusion, cauliflower LAA morphology is associated with an increased risk of CETIA and CES through its large LAA orifice diameters and low LAA flow velocity. There are clear differences in LAA orifice diameters and flow velocity among patients with AF alone, CES, and CETIA.