Atrophic gastritis can cause mucosa thinning, while detailed metrological evidence is lacking. We aimed to compare the morphological features of full-thickness gastric mucosa in antrum and corpus and evaluate the diagnostic performance for atrophy. Gastric cancer patients were prospectively enrolled (N = 401). Full-thickness gastric mucosa was obtained. Foveolar length, glandular length and musculus mucosae thickness were measured. Pathological assessment was conducted using the visual analogue scale of the updated Sydney system. Areas under the receiver operating characteristic curves (AUCs) were calculated for different atrophy degrees. In corpus mucosa, foveolar length and musculus mucosae thickness were positively correlated with the atrophy degree (spearman's correlation coefficient [rs] = 0.231 and 0.224, respectively, P < .05); glandular length and total mucosal thickness were negatively correlated (rs = -0.399 and -0.114, respectively, P < .05). Total mucosal thickness did not correlate with antral atrophy degree (P = .107). The AUCs of total mucosal thickness for corpus and antral atrophy were 0.570 (P < .05) and 0.592 (P < .05), respectively. The AUCs for corpus atrophy, moderate and severe, and severe atrophy were 0.570 (P < .05), 0.571 (P = .003), and 0.584 (P = .006), respectively. The corresponding AUCs for antral atrophy were 0.592 (P = .010), 0.548 (P = .140), and 0.521 (P = .533), respectively. The tendency for mucosal thickness to thin with atrophy occurred in the corpus rather than in the antrum. The diagnostic performance of corpus and antral mucosal thickness was limited for atrophy.Copyright © 2023 the Author(s). Published by Wolters Kluwer Health, Inc.