Objective To investigate the gastroscopy, pathological and immunohistochemistry characteristics of upper gastrointestinal GIST, in order to improve the recognition and diagnosis of endoscopic doctor of the disease, reduce misdiagnosis and missed diagnosis. Methods Clinical manifestation, endoscopy, operation pathology and immunohistochemical data of 30 upper gastrointestinal GIST from January 2007 to April 2010 of Peking University People’s hospital were analyzed retrospectively. Results The main clinical manifestations of GIST included gastrointestinal hemorrhage in 11 cases (36.7%), abdominal pain in 6 cases (20%), abdominal discomfort in 4 cases (13.3%). Of the 30 cases of GIST, 12 (40%) were at the fundus, 7 (23.3%) were at the body. Endoscopically, in 30 GIST patients, 12 cases showed submucosal protuberant global or half-global lesions;7 cases were presented as submucosal protuberant with ulcer;4 cases were ulcer-like tumors;3 cases were submucosal protuberant with hollow on the top; 1 case was the submucosal surface erosion and proliferation; 2 cases were submucosal protuberant with erosion; 1 case was negative. 14 cases underwent endoscopic ultrasonography, most cases of the stromal tumors were from muscularis. Pathology revealed the typical stromal tumor features with cell in spindle shape. Immunohistochemical examination demonstrated CD117 positive rate was 96.7% (29/30), CD34 positive rate was 90% (29/30). Conclusion Most clinical manifestation of upper gastrointestinal GIST were gastrointestinal bleeding and abdominal pain, abdominal discomfort. Gastroscopic features of GIST were varied. Most were submucosal protuberant, 40%cases ofthe surface were smooth, 56.7%cases of surface with erosion or ulcer. A few cases of tumor, the surface present proliferation, it’s difficult to distinguish from cancer. The diagnosis rate of endoscopic ultrasound was satisfied.