We report here a case of a gastrointestinal stromal tumor (GIST) in the stomach that was diagnosed by endoscopic ultrasound-guided fine needle aspiration cytology (EUS-FNA). A 67 year old male patient underwent regular check-ups for five years due to the presence of a submucosal tumor that was found in the fundus of the stomach incidentally. EUS-FNA was performed to evaluate the tumor, which had increased in size from 1 cm to 2.8cm. A cytologic smear revealed cohesive sheets or clusters of spindle cells with elongated nuclei. Immunohistochemical staining revealed a strong positive reaction for c-kit and CD34, without any reaction for smooth muscle actin and Ki-67. Therefore, a diagnosis of GIST was made.