Herein, we aimed to examine the diagnostic yield and utility of boring biopsy for subepithelial lesions (SEL) of the stomach and esophagus. A total of 52 patients with SELs of the stomach or esophagus underwent boring biopsy. The diagnostic yield of boring biopsy for gastric and esophageal SELs was 50% (21/42) and 80% (8/10), and for SELs with a diameter of less than 10mm, the diagnostic yield was 67% (6/9) and 83% (5/6), respectively. Forty-three percent (9/21) of the gastric SELs were diagnosed with gastrointestinal stromal tumor (GIST), while all esophageal SELs (8/8) were leiomyomas. Ten percent (4/42) of boring biopsies for the stomach were accompanied by complications:two cases of perforation and two of bleeding.