Background: Left atrial appendage (LAA) dysfunction is an independent predictor of thromboembolism in mitral stenosis (MS). Objectives: To investigate whether there is a relation between annular velocities obtained by tissue Doppler imaging and LAA function and to determine if the annular velocities can predict the presence of the inactive LAA in MS. Methods: Eighty-five MS patients and 80 healthy controls were evaluated by transthoracic echocardiography and all patients underwent transesophageal echocardiography. The annular systolic (S-wave) and diastolic (E- and A-waves) velocities were recorded. Inactive LAA was defined as LAA emptying velocity < 25 cm/sec. Patients were divided into three groups; group I (n = 43): sinus rhythm (SR) and LAA emptying velocity >= 25 cm/sec, group II (n = 15): SR and LAA emptying velocity < 25cm/sec and group III (n = 27): atrial fibrillation. Results: Thrombus was detected in 12 patients and spontaneous echo contrast (SEC) was detected in 48 patients. Both S-wave and peak LAA emptying velocities were decreasing, while SEC frequency and density were increasing from group I to group III. There was a positive correlation between LAA emptying and S-wave velocities (P < 0.001, r = 0.682). Multivariate regression analysis showed that only S-wave is the independent predictor of inactive LAA (P = 0.001, odds ratio = 0.143, 95% CI = 0.047-0.434). In patients with SR, the cutoff value of S-wave was 13.5 cm/sec for the prediction of the presence of inactive LAA (sensitivity: 95.3%, specificity: 93.3%). Conclusions: S-wave is an independent predictor of inactive LAA and a useful parameter in estimating inactive LAA in MS with SR.