The detection of a thrombus at the left atrial appendage (LAA) is an important step for management in a patient with a suspected embolic infarction. However, spontaneous echocardiographic contrast (SEC), which can mimic thrombus, can confuse clinicians in many cases. We examined electrocardiographic-gated 64-slice multidetector computed tomography with a 2-phase scan and transesophageal echocardiography in 314 patients with suspected embolic stroke. The transesophageal echocardiographic findings were classified using a 5-grade scale and the multidetector computed tomographic findings were categorized as no filling defect, an early filling defect (a filling defect seen on early-phase images without considering the late-phase images), and a persistent filling defect (a filling defect seen on added late-phase images, as well as on early-phase images). For quantitative analysis, the ratio of Hounsfield units in the LAA to the ascending aorta (AA) was calculated for each early-phase and late-phase image (LAA/AA_L). Using transesophageal echocardiography as the reference standard, for no filling defect seen on early-phase images, the presence of a thrombus, including severe SEC, could be ruled out with 100% sensitivity and a 100% negative predictive value. When considering the addition of late-phase images, all persistent filling defects had resulted from the presence of a thrombus and severe SEC. However, using the optimal cutoff value of 0.5 for the LAA/AA_L ratio, thrombi could be distinguished from severe SEC where all thrombi had a LAA/AA_L ratio <0.5. In conclusion, our findings suggest that 2-phase multidector computed tomography is useful for the detection and differentiation of a thrombus from SEC at the LAA in patients with suspected embolic stroke.