Previous reports did not encourage balloon mitral commissurotomy (BMC) when left atrial (LA) thrombi were located beyond LA appendage. We hypothesize that LA thrombi may be resolved in some patients after anticoagulant therapy, and BMC can be performed subsequently. In the present study, we used transesophageal echocardiography (TEE) to evaluate the effects of anticoagulant on LA thrombi in patients with mitral stenosis, to compare the clinical differences between patients with (group A) and without (group B) resolution of LA thrombi, and to evaluate the safety of subsequent BMC in these patients. TEE was performed on 190 consecutive patients with mitral stenosis; 14 (7.4%) of them were found with LA thrombi. Serial TEE was performed and optimal anticoagulant therapy was achieved in all 14 patients. The thrombi were located within the LA appendage in 6 cases, attached to the LA posterior wall in 5, posterior wall and interatrial septum in 1, and LA appendage and posterior wall in 2. Based on the 6-month TEE follow-up, we found that the LA thrombi disappeared in 8 (57.2%) patients (group A) and persisted in 6 patients (group B). LA thrombi resolved within 3 months in 7 group A patients (87.5%). Furthermore, the resolution of LA thrombi was more frequently observed in patients either with a smaller LA dimension (51.9 ± 3.4 vs. 57.8 ± 4.8 mm, p = 0.02) or with their thrombi located inside their LA appendage (p = 0.03). No differences in other clinical and echocardiographic variables were noted between these two groups. Subsequently, group A patients underwent BMC without complications of systemic embolization. In conclusion, LA thrombi can be resolved after optimal anticoagulant therapy in a considerable proportion of patients with mitral stenosis. Serial TEE studies are helpful to observe LA thrombus resolution; they may also be useful in planning the treatment strategy.