Objective To compare the pathological results between preoperative gastroscopy samples and postoperative samples of endoscopic resection from patients with gastric intraepithelial neoplasia, and further investigate the risk factors of pathological upgrading. Methods A retrospective analysis was performed on the data of 371 patients with gastric intraepithelial neoplasia confirmed by biopsy and undergoing endoscopic resection from January 2012 to December 2014 in Nanjing Drum Tower Hospital. The preoperative and postoperative pathological results were compared, and the risk factors for pathological upgrading after operation were analyzed. Results Among 371 patients, 173 and 198 cases were diagnosed as low-grade intraepithelial neoplasia ( LGIN ) and high-grade intraepithelial neoplasia ( HGIN ) , respectively, by preoperative endoscopic biopsy. By postoperative pathology of endoscopic resection, 113 ( 65. 3％) of 173 LGIN cases kept the diagnosis, while 46 ( 26. 6％) of 173 cases were upgraded to HGIN, and 10 ( 5. 8％) of 173 cases were finally upgraded to gastric cancer. The upgrade rate was 32. 4％(56/173). In the HGIN group, 107 ( 54. 0％) of 198 HGIN patients had the same diagnosis after endoscopic resection, 78 ( 39. 4％) of 198 cases were upgraded to cancer. Multivariate regression analysis showed that diameter of larger than 2 cm (P=0. 008), proximal stomach location (P=0. 011), mucosal surface redness ( P=0. 000 ) , and surface depression or ulcer ( P=0. 003 ) were independent factors of pathological upgrading for postoperative samples. Conclusion Preoperative biopsy for the diagnosis of gastric intraepithelial neoplasia has a certain misdiagnosis rate. More attentions should be paid on the lesion which is larger than 2 cm in diameter, located in the proximal stomach, or mucosa with red surface, depression or ulcer. Postoperative pathological examination can help to clarify the nature of the lesion.