We investigated the clinicopathological characteristics of EBV-associated gastric cancers among poorly differentiated gastric adenocarcinomas. A total of 412 patients with poorly differentiated gastric adenocarcinoma were studied for Epstein-Barr virus (EBV) infection by in situ hybridization for EBV-encoded small RNA. EBV genomes were detected in the tumor cell nuclei of 83 gastric cancers (20.1%). Of these EBV-positive cancers, 60 were histologically classified as gastric carcinoma with lymphoid stroma. Comparing various clinicopathological data with EBV status in gastric cancers revealed a significantly large discrepancy between the clinical and pathological lymph node evaluation of the EBV-positive cancers as compared with that of EBV-negative cancers. These results indicated that a strong host immune reaction occurs in the regional lymph nodes of EBV-associated gastric cancers, and that surgeons should be warned against clinically overestimating the stage of EBV-associated gastric cancer.