AbstractAbnormalities of the AT‐rich interaction domain 1A (ARID1A) occur in cancer tissues and precursors or premalignant lesions in various organs. To investigate the significance of ARID1A abnormalities in the early phase of cancer development in the stomach, we screened for ARID1A loss and p53 overexpression in glands in non‐neoplastic gastric mucosa using immunohistochemistry. We tested 230 tissue blocks of 77 patients with gastric carcinoma, and in 10% of non‐neoplastic mucosa we detected ARID1A‐lost and in 3.7% p53‐overexpressed foci. Loss of ARID1A expression occurred in the scales of several glands, which were morphologically characterized as authentic, pseudo‐pyloric, or intestinal metaplastic glands devoid of dysplastic changes. In contrast, p53‐overexpressed foci were detected in dysplastic intestinal metaplasia. In early gastric cancer cases (n = 46), ARID1A‐lost foci were frequent in samples of patients with Epstein–Barr virus‐associated gastric carcinoma (p = 0.037). Ultra‐deep DNA sequencing of ARID1A‐lost foci revealed frameshift and nonsense mutations in ARID1A. Mapping abnormal glands in the entire resected stomach of the three selected patients demonstrated that ARID1A‐lost foci clustered with p53 abnormal glands. ARID1A‐lost epithelial cells may develop clonal growth through the pathway, different from p53‐abnormal intestinal metaplasia, and require one or more events to develop into an overt carcinoma, such as EBV infection.