Most of the submucosal lesions encountered on endoscopy are benign; however, the fact that some of them may be malignant considerably influences the attitude toward the whole group. This article reviews the current status of endosonography in the management of submucosal lesions and focuses on determining the risk of malignancy. The predictive value of various endoscopic ultrasonography (EUS) features and their combinations and the capabilities and limitations of EUS-guided fine needle biopsy are discussed. Other issues addressed include differentiation between extraluminal compressions and true submucosal lesions, EUS-assisted endoscopic removal of submucosal lesions, and the potential role of catheter-based endosonography in the setting of submucosal lesions. Problems related to the surveillance of patients with submucosal lesions who are not candidates for surgical treatment are outlined. An overview of the recent changes in the pathologic classification of gastrointestinal mesenchymal tumors and their impact on the role of EUS in the management of submucosal lesions is given.