Data regarding the in-depth surface marker profiles of gastric tissue-resident lymphocytes in autoimmune and Helicobacter pylori-associated gastritis are lacking. In this study, we investigated potential differences in lymphocyte composition between these profiles. We enrolled patients with autoimmune (n = 14), active (current infection of H. pylori in the stomach; n = 10), and inactive gastritis (post-eradication of H. pylori; n = 20). Lymphocytes were isolated from the greater curvature of the stomach and lesser curvature of the body and analyzed using flow cytometry. The CD8⁺/CD3⁺ and CD4⁺/CD3⁺ ratios differed between the samples. Body CD4⁺/antrum CD4⁺, which is calculated by dividing the CD4⁺/CD3⁺ ratio in the body by that in the antrum, was significantly higher in autoimmune gastritis (3.54 ± 3.13) than in active (1.47 ± 0.41) and inactive gastritis (1.42 ± 0.77). Antrum CD8⁺/CD4⁺ in autoimmune gastritis (7.86 ± 7.23) was also higher than that in active (1.49 ± 0.58) and inactive gastritis (2.84 ± 2.17). The area under the receiver operating characteristic curve of antrum CD8⁺/CD4⁺ was 0.842, and the corresponding optimal cutoff point was 4.0, with a sensitivity of 71.4% and a specificity of 93.3%. We propose that an antrum CD8⁺/CD4⁺ ratio > 4.0 is a potential diagnostic marker for autoimmune gastritis.