Aim Vitamin B12 deficiency is frequent in older patients, and the main reason is pernicious anemia. However, vitamin B12 deficiency can occur in patients who do not have atrophic gastritis. The aim of the present study was to investigate factors affecting serum vitamin B12 levels in older patients with non‐atrophic gastritis. Methods A total of 1256 out of 1607 patients aged over 60 years who had undergone upper gastrointestinal endoscopy for various reasons, and who had serum vitamin B12 value and were diagnosed as having “non‐atrophic gastritis” were analyzed by means of factors affecting low serum vitamin B12 levels. Results Non‐atrophic gastritis patients were divided into two groups: patients with normal serum vitamin B12 (group I, n = 759) and patients with low serum vitamin B12 (group II, n = 497). The median serum vitamin B12 was 339 pg/mL (range 201–987 pg/mL) in group I and 180 pg/mL (range 50–200 pg/mL) in group II. Helicobacter pylori (n = 154 vs 325, P < 0.001), neutrophil activity (n = 176 vs 367, P < 0.001), intestinal metaplasia (n = 35 vs 14, P < 0.001) and inflammation (n = 230 vs 386, P < 0.001) were present significantly more often in group II compared with group I. A total of 785 patients were both negative for Helicobacter pylori and atrophy. Of these 785 patients, neutrophil activity (n = 56, [32.6%] vs 25, [4.4%], P < 0.001) and inflammation (n = 69, [40.1%] vs 82, [13.4%], P < 0.001) scores were present significantly more often in group II compared with group I. Conclusions Helicobacter pylori was present significantly more often in older patients whose serum vitamin B12 levels were ≤200 pg/mL, and Helicobacter pylori density was inversely correlated with serum B12 level. Upper gastrointestinal endoscopic examination should be suggested for elderly patients with serum vitamin B12 level ≤200 pg/mL. Geriatr Gerontol Int 2015; ●●: ●●–●●.