Endoscopic ultrasonography (EUS) is the most accurate procedure for detecting and diagnosing subepithelial tumors, due to its higher sensitivity and specificity than other imaging modalities. EUS can characterize lesions by providing information on echogenic origin, size, borders, homogeneity, and the presence of echogenic or anechoic foci. Linear echoendoscopes, and recently also electronic radial echoendoscopes, can be used with color Doppler or power Doppler to assess the vascular signals from subepithelial masses, and thus permit the differentiation of vascular structures from cysts, as well as the assessment of the tumor blood supply. However, the diagnostic accuracy of EUS imaging alone has been shown to be low in subepithelial lesions with 3rd and 4th layers. It is also difficult to differentiate exactly between benign and malignant tumors and to gain an accurate picture of histology using EUS. On the other hands, EUS guided fine needle aspiration (EUS-FNA) can provide samples for cytologic or histologic analysis. Hypoechoic lesions of the 3rd and the 4th EUS layers, more than in 1 cm diameter are recommended, and histologic confirmation using endoscopic submucosal resection or EUS-FNA should be obtained when possible. Therefore, EUS-FNA plays an important role in the clinical management of subepithelial tumors. Furthermore improvements in endoscopic technology are expected to be more useful modalities in differential diagnosis and discrimination between benign and malignant subepithelial tumors.