OBJECTIVE To diagnose and characterize subepithelial lesions of the gastrointestinal (GI) tract using endoscopic ultrasonography (EUS) and search for markers of malignancy in stromal cell tumors. METHODS Fifty-four patients with suspected subepithelial lesions at endoscopy were examined using miniature ultrasound probes, integrated ultrasound endoscopes, or both. Surgical treatment was considered if a solid lesion had a maximum diameter of at least 3 cm, mixed echogenicity, or an ill-defined or irregular border. RESULTS EUS disclosed 37 solid lesions and ten fluid-filled structures. In seven patients, including two with protrusion from a normal spleen, no pathology could be demonstrated. Thirteen patients were operated and 41 were observed clinically with (n = 9) or without EUS (n = 32) for a median follow-up period of 36 months. Twenty-three patients had an intramural stromal cell tumor. None of these were malignant, but increased mitotic activity was found in two medium-sized resected tumors with mixed echogenicity and bleeding lesions of the endoluminal surface. CONCLUSIONS EUS can detect and characterize subepithelial masses in the GI tract. Pathologic lesions of the overlying mucosa may indicate malignant development in stromal cell tumors, but valid markers of malignant potential are still lacking.