Gastrointestinal stromal tumor (GIST) of the duodenum is rare. Obtaining tissue samples of GIST in the duodenum is difficult, especially when the tumor is located in the distal duodenum. Thus, preoperative pathological diagnosis often becomes difficult. We performed endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) biopsy for two cases with submucosal tumors in the third portion of the duodenum. Tissue samples were successfully obtained and diagnosed as GIST. Partial duodenectomy was performed in the two patients. Thus, we believe that EUS-FNA is a potentially useful diagnostic aid for submucosal tumors in the third portion of the duodenum, and it should be attempted before more invasive approaches.