Epstein-Barr virus (EBV)-associated gastric cancer (GC) and microsatellite-instability-high GC are associated with a low prevalence of regional lymph node metastasis (LNM). To evaluate the feasibility of endoscopic treatment of EBV-associated and/or microsatellite-instability-high early GC (EGC), we analyzed the risk factors for LNM using a large series (n=756) of submucosa-invasive (SM) EGC. EBV-encoded RNA in situ hybridization (EBER ISH) and immunohistochemistry for four mismatch repair (MMR) proteins (MLH1, PMS2, MSH2, and MSH6) were performed. The clinicopathologic features and results of EBER ISH and immunohistochemistry were compared according to the LNM status. Among the cases, 146 EGCs (19.3%) showed LNM. EBV negativity, larger tumor size (greater than 2cm), deeper level of submucosal invasion, submucosal invasion depth greater than 500µm, presence of ulceration, and presence of lymphovascular invasion (LVI) were associated with LNM. However, the MMR deficiency was not correlated with LNM. On multivariate regression analysis, larger tumor size (greater than 2cm; odds ratio1.6, p=0.030), deeper level of submucosal invasion (odds ratio2.9, p=0.001), LVI (odds ratio 7.4, p<0.001), and EBV negativity (p=0.020) were independent risk factors for LNM in SM EGCs. EBV positivity was a favorable risk factor for LNM in SM EGC. However, MMR deficiency was not associated with the status of LNM. Thus, we suggest that examination with EBER ISH could be considered for endoscopic resected specimens, especially in cases of SM EGC showing no LVI and clear resection margins.