Transesophageal echocardiogram (TEE) is a gold standard test for diagnosis of left atrial (LA) thrombus, but it has limited sensitivity for identification of small thrombi within side lobes. Thus, the absence of visualizing a left atrial appendage (LAA) thrombus does not equate with the absence of a LAA thrombus. To assess the predictive value of mitral annular systolic velocity (Sa) and D-dimer for the detection of LA thrombus and spontaneous echocardiographic contrast (SEC) in mitral stenosis (MS) patients with sinus rhythm (SR). Transthoracic echocardiogram, TEE, and D-dimer analysis were performed in 104 severe MS patients and divided them into three groups: Group I:no LA thrombus or SEC; Group II:LA SEC only; and Group III:LA thrombus. Group III had more severe New York Heart Association (NYHA) class (III-IV) dyspnea and lower Sa (6.9 ± 0.7 vs.10.0 ± 1.2 cm/sec), lower LAA late emptying velocity (17.7 ± 2.1 vs. 24.4 ± 4.2 cm/sec), larger LA transverse dimension, and LAA area (LAAA) than group I+II. Mean D-dimer levels were higher in groups III and II than in group I. In multivariate analysis Sa, D-dimer levels, LAAA, and NYHA class were independent predictors of LA thrombus. ROC curve analysis revealed that higher Sa >8 cm/sec and lower D-dimer levels <370 μg/L predict the absence of LA thrombus and lower Sa <8 cm/sec and higher D-dimer levels >510 μg/L predict the presence of LA thrombus. Measurement of Sa and D-dimer levels is necessary for better assessment of LA thrombus and SEC, for identification of patients who are at high risk for LA thrombus formation and for initiation of prophylactic anticoagulation.