Background/Aims: This study aimed to evaluate the prevalence and natural progression of subepithelial lesions (SELs) in the upper gastrointestinal (UGI) tract.Methods: The medical records of patients with UGI SELs who underwent endoscopic screening at eight university hospitals between January and December 2010 were retrospectively investigated. The follow-up evaluations were performed until December 2016.Results: UGI SELs were found in 1,044 of the 65,233 participants screened (endoscopic prevalence, 1.60%; the total number of lesions, 1,062; mean age, 55.1±11.2 years; men, 53.6%). The median follow-up period was 48 (range, 8–74) months. SELs were most frequently found in the stomach (63.8%) and had a mean size of 9.9±6.1 mm. Endoscopic ultrasonography (EUS) was performed in 293 patients (28.1%). The most common lesions were leiomyomas, followed by gastrointestinal stromal tumors (GISTs), and ectopic pancreas. The proportions of SELs with malignant potential according to size were 3% (<1 cm), 22% (1–2 cm), 27% (2–3 cm), and 38% (≥3 cm). In gastric SELs larger than 1 cm, resections were performed in 20 patients because of an increase in size, of which 12 were found to be GISTs.Conclusions: The prevalence of UGI SELs was 1.60%. Further, 23% of gastric SELs ≥1 cm were precancerous lesions, most followed by EUS and clinical decisions without initial pathological confirmation.