Background S-1 is an oral anticancer drug widely used in postoperative adjuvant therapy for patients in Japan with stage II/III gastric cancer. Candidates for more intense adjuvant treatments need to be identified, particularly among patients with stage III cancer. Methods Univariate and multivariate analyses were conducted for patients with stage II/III gastric cancer who underwent surgery and received S-1 postoperatively between 2000 and 2010.Results Factors indicating poor prognosis identified by univariate analysis include male sex (P = 0.022), age C67 years (P = 0.021), intestinal-type histology (P = 0.049), lymph node ratio C16.7 % (P \ 0.0001), open surgery (P = 0.039), as well as the 13th JGCA stage (P \ 0.0001) and the 14th JGCA/7th International Union Against Cancer (UICC) stage (P \ 0.0001). Multivariate analysis revealed that lymph node ratio C16.7 % and intestinal-type histology were significant as predictors of prognosis, independent from the pathological stages. Based on these and other findings, stage IIIC cancer on the 14th JGCA/7th UICC stage system in combination with the lymph node ratio could identify patients with extremely high risk for recurrence Conclusions Our current findings suggest that lymph node ratio C16.7 % in combination with the new staging system could be a useful prognostic indicator in advanced gastric cancer. Because these high-risk patients cannot be identified preoperatively by any diagnostic tool, further improvement in postoperative adjuvant therapy is warranted.