Background: Chronic atrophic gastritis (CAG) are closely related to the development of gastric cancer. However, the diagnostic accuracy of white light endoscopy (WLE) biopsy for CAG is poor. The diagnostic role and efficacy of confocal laser microscopy (CLE) in CAG missed under WLE biopsy remains unclear.Methods: This study is a single-center prospective study that included 21 patients who were diagnosed with CAG under WLE, and whose pathological results were chronic inflammation. Then, all these patients received a CLE examination and endoscopic features were evaluated. All patients underwent targeted biopsies and five-point standard biopsies under CLE. The sensitivity, specificity, and accuracy of CLE diagnosis and targeted biopsy were analyzed by using the five-point standard biopsy pathological results.Results: The pathological results of five-point standard biopsies in 21 patients were CAG, and 17 patients (81.0%) were intestinal metaplasia (IM). According to the image diagnosis under CLE, 19 of these 21 patients (90.5%) were diagnosed with CAG, and 14 of them (66.7%) were diagnosed with IM. According to the targeted biopsy under CLE, 17 (81.0%) patients were diagnosed with CAG, and 14 of them (66.7%) were diagnosed with IM. There was no significant difference between CLE image diagnosis and five-point standard biopsies in terms of atrophy severity score (p=0.927), IM severity score (p=0.250), atrophy scope score (p=0.781) and IM scope score (p=0.195). For CAG, the sensitivity and accuracy of CLE image diagnosis were higher than those of CLE targeted biopsies (90.5% vs. 81.0%, p=0.331). For IM, the sensitivity, specificity and accuracy of CLE image diagnosis were the same as those of CLE targeted biopsies.Conclusions: CLE can improve the diagnosis rate of CAG, and can increase the comprehensive assessment of the scope and severity of CAG.