Incidental gastric subepithelial tumor (SET) is frequently found during endoscopy. Although endoscopic ultrasonography (EUS) can provide useful information, its diagnostic accuracy varies. Most of the potentially malignant tumors observed on EUS are hypoechoic lesions. Therefore, we aimed to investigate the diagnostic accuracy of EUS for hypoechoic lesions located in the submucosa or proper muscle layer. We also evaluated various characteristics for potential associations with diagnostic accuracy.A retrospective review was conducted of the medical records of 99 patients who were diagnosed with gastric SET and who underwent EUS with pathologic confirmation between March 2008 and April 2015. After reviewing the endoscopic and pathologic findings, we attempted to analyze factors that were associated with the diagnostic accuracy of EUS.The mean ± standard deviation size of the lesions was 20.0 ± 12.7 mm. The most common location was the upper third of the stomach (43.4%). The overall accuracy of EUS was 66.7%. No statistically significant difference in EUS accuracy was observed according to the location, size, or layer of the lesion. The following pathologic diagnostic methods were used: EUS-guided fine needle aspiration (3.0%), forceps biopsy (16.2%), deep tissue biopsy using cap-assisted mucosal resection (8.1%), endoscopic submucosal dissection (25.2%), and operation (47.5%). The accuracy of EUS according to the expected diagnosis of the lesion was 77.1% for gastrointestinal stromal tumor, 50% for neuroendocrine tumor, and 50% for ectopic pancreas.Although EUS is a useful tool for gastric SET in clinical practice, the accuracy of diagnostic EUS is suboptimal. When considering whether to treat gastric SET, the decision should be made based on the pathologic diagnosis.