Endoscopic ultrasound-guided fine needle aspiration biopsy (EUS-FNA) is considered to be a reliable and accurate method for the evaluation of submucosal lesions in the gastrointestinal tract. Herein, we report our experience with the diagnosis of 10 cases of gastrointestinal stromal tumor (GIST) using EUS-FNA. The materials obtained from the EUS-FNA were stained with the rapid Romanowsky or the Papanicolaou method for cytologic examination. The subsequent surgical resection specimens were submitted for histopathologic examination. Immunoperoxidase stains were performed on the cell blocks and/or representative histologic sections of the tumor using commercially available antibodies against c-kit (CD117), CD34, S-100, and smooth muscle actin. Of the 10 cases studied, there were five men and five women with an average age of 62 years (range, 38 to 87 years). Five tumors were located in the stomach, and five in the duodenum. Tumor size ranged from 3.5 to 16.2 cm. Immediate on-site evaluation and cytologic diagnoses were given in eight cases (80%) with an average of three passes. The diagnoses were confirmed by strong and diffuse tumor cell c-kit immunoreactivity in the cell blocks. However, the final diagnoses of two other cases (20%) were not established until surgical resections were obtained. Retrospectively, reviews of cytologic smears of both cases demonstrated rare cohesive sheets or clusters of spindle cells with cigar-shaped nuclei. These observations were initially misinterpreted as benign fibrous tissue and/or fragments of smooth muscle of the gastrointestinal wall such as one might encounter in a routine transgastric or transduodenal EUS-FNA. The current study showed that when combining cytologic and immunocytochemical studies, EUS-FNA is accurate and efficient in the diagnosis of GIST. It exemplified the importance of considering GIST in the differential diagnosis of gastrointestinal lesions and also demonstrated the potential pitfalls of EUS-FNA evaluation of submucosal lesions in the gastrointestinal tract. Copyright 2002, Elsevier Science (USA). All rights reserved.