BACKGROUND/AIMS: In this study we aimed to determine the rate of concordance of endoscopic ultrasonography (EUS)-guided fine needle aspiration (FNA) diagnosis with the final diagnosis obtained by surgery or endoscopic resection and follow-up in upper gastrointestinal subepithelial lesions. METHODS: We retrospectively studied patients with subepithelial lesions who underwent EUS at our center from 2007 to 2011. RESULTS: We had a final diagnosis in 67 patients (mean age+/-SD, 51.23+/-12.48 years; 23 [34.3%] female, 44 [65.6%] male). EUS-FNA was performed in all of the patients. On-site pathology was not performed. In nine of the patients, the obtained material which was obtained was insufficient. The cytologic examination was benign in 31 and malignant in 27 of the patients. Based on the final diagnosis, the EUS-FNA had a sensitivity of 96%, a specificity of 100%, and a diagnostic yield of 85%. CONCLUSIONS: The diagnostic yield of EUS-FNA, in the absence of the on-site cytopathologist, is feasible for the diagnosis of subepithelial lesions of the upper gastrointestinal system.