Limited studies investigated clinicopathological and prognostic significance of histologic and molecular subgroups of gastric cancer concurrently. We retrospectively enrolled 1,248 patients with gastric cancer who received radical gastrectomy with lymphadenectomy and classified these cases into the EpsteinâBarr virus (EBV)âassociated and microsatellite instability (MSI)âassociated subtypes by EBVâencoded small RNA in situ hybridization and immunohistochemical stains for DNA mismatch repair proteins, respectively. The remaining cases were categorized as the Lauren intestinal and diffuse/mixed subtypes. The clinicopathological and prognostic significance of the subtypes was examined by statistical analysis. In total, 65 (5.2%), 116 (9.3%), 496 (39.7%), 431 (34.5%) and 140 (11.2%) cases were identified as EBVâassociated, MSIâassociated, intestinal, diffuse and mixed subtypes, respectively. The EBVâassociated, MSIâassociated, intestinal and diffuse/mixed subtypes exhibited distinctive clinicopathological characteristics, including differences in age, gender, stump cancer, gastric location, tumor size, TNM stage, margin involvement, lymphatic/perineural invasion, HER2 status and recurrence pattern. The logârank test showed survival discrimination (pâ<â0.001), and the multivariate analysis identified EBVâassociated and MSIâassociated cases demonstrated better outcomes than the diffuse/mixed subtype (EBV, HR 0.464, 95% CI 0.296â0.727, pâ=â0.001; MSI, HR 0.590, 95% CI 0.407â0.856, pâ=â0.005). EBVâassociated lymphoepitheliomaâlike carcinoma cases had the most favorable outcome (HR 0.138, 95% CI 0.033â0.565, pâ=â0.006). In different clinical groups, the subtypes exhibited survival discrepancies. The EBVâassociated and diffuse/mixed cases exhibited more favorable response to chemotherapy. In conclusion, this combined classification, in parallel with the molecular subtypes specified in the Cancer Genome Atlas study, has implications for the clinical management of gastric cancer.