Abstract Initial diagnosis of submucosal gastrointestinal stromal tumors (GISTs) is often made from material obtained by endoscopic ultrasound–guided fine-needle aspiration (EUS-FNA). Although 95% of GISTs are positive for KIT by immunohistochemical analysis on surgical specimens, we have observed several cases of GIST that were negative for KIT on the cell block but subsequently positive on the surgical resection. DOG1 has been found to be a specific and sensitive marker for GISTs on surgical material. We compared KIT and DOG1 staining in 52 GIST cell blocks and in 44 cell blocks of other intra-abdominal spindle cell neoplasms. We found that DOG1 was the more sensitive marker, with positivity in all 52 GIST cell blocks. KIT was positive in 46 (88%) of the GIST cases, with sensitivity dependent on the FNA method. Both markers were highly specific: KIT was negative in all 44 non-GIST cases, whereas DOG1 showed weak positivity in only 1 leiomyosarcoma.