I have previously reported the efficacy of whole stomach observation using magnifying narrow-band imaging at low magnification (LM-NBI) after routine white light imaging (WLI). LM-NBI detects lesions missed on WLI. However, the validity of annual examinations are yet to be elucidated. This historical case-control study was conducted on patients with chronic gastritis at a single institution. The patients were divided into two groups: the LM-NBI group, which include patients who underwent whole stomach observations with LM-NBI, defined as the minimal magnification required to reveal the microsurface pattern of the gastric mucosa after WLI; and the conventional endoscopy (CE) group as the control. Investigations included an index endoscopy followed by approximately five annual endoscopes. A total of 388 patients were assigned to the LM-NBI group, whereas 381 were to the CE group. Fifteen cases of gastric neoplasia were identified in the LM-NBI group, and five cases in the CE group. A hazard ratio of 2.78 (95% CE, 1.01 to 7.64) was determined using a Cox proportional-hazards model, and using Kaplan–Meier analysis (p = 0.039, by log-rank test), annual LM-NBI was superior to CE in detecting gastric neoplasia. This is the first study to report the efficacy of annual endoscopies using LM-NBI.