AIM: to evaluate the role of endoscopic ultrasonographyguided fine needle aspiration (EUS-FNA) in the preoperative diagnosis of gastrointestinal stromal tumor (GIST).METHODS: From September 2002 to June 2006, Fiftythree consecutive EUS-FNAs of GI tract subepithelial hypoechoic tumors with continuity to proper muscle layer suspected as GIST by standard EUS were evaluated prospectively. The reference standards for the final diagnosis were surgery (n = 31), or clinical follow-up (n = 22). Additionally, immunophenotyping of specimens obtained by EUS-FNA and surgical resection specimens were compared.RESULTS: In 2 cases puncture was not performed because of anatomical problems. The collection rate of adequate specimens from the GI tract subepithelial hypoechoic tumor with continuity to proper muscle layer was 82% (42/51). The diagnostic rate for the tumor less than 2 cm, 2 to 4 cm, and 4 cm or more were 71% (15/21), 86% (18/21), and 100% (9/9),respectively. In 29 surgically resected cases, the sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of EUS-FNA using immunohistochemical analysis of GIST were 100%(24/24), 80% (4/5), 96% (24/25), 100% (4/4), and 97% (28/29), respectively. No major complications were encountered.CONCLUSION: EUS-FNA with immunohistochemical analysis is a safe and accurate method in the pretherapeutic diagnosis of GIST. It should be taken into consideration in decision making, especially in early diagnosis following minimal invasive surgery for GIST.