Abstract: Objective: To study the morphological characteristics of gastric mucosa atrophy under confocal laser endomicroscope（CLE） and the possibility and accuracy of CLE in diagnosis of gastric mucosa atrophy accompanying intestinal metaplasia in vivo. Methods: A total of 42 patients with a history of gastric mucosa atrophy accompanying intestinal metaplasia（IM） underwent routine endoscopy and CLE,respectively.Images obtained from each site were stored and samples were obtained at the same location for biopsies.The endoscopic images,confocal endoscopic images and biopsy pathology were compared,respectively. Results: A total of 7 200 confocal endoscopic images were obtained from 42 patients.The gastric pits,columnar epithelial cells,connective tissue and capillaries could be clearly observed.Under CLE,reduced mucosal glands and enlarged space of mucosal pits were found in gastric mucosal atrophy.Confocal endoscopic images showed that gastric mucosal atrophy was decreased in gastric pits.The goblet cells were easily distinguished on the CLE images,showing the feature of IM.The sensitivity,specificity and accuracy of CLE for gastric mucosa atrophy accompanying IM were 88%,87%,and 88%,respectively,while those of routine endoscopy were 44%,16%,and 28%,respectively. Conclusion: CLE is a novel diagnostic tool to enable virtual histology in vivo during ongoing endoscopy,and has a high diagnostic accuracy of gastric mucosa atrophy accompanying IM.