Gastric cancer patients with the same clinical stage may vary greatly in prognosis, which makes the improvement of current staging-based treatment imperative. The systematic biology approaches are the solution for systematic identification of biomarkers for prognostic evaluation and targeted therapy. These markers will be applied to classify the patients by molecular traits and then to guide the individualized medication. Although HER-2 antibody is currently the only targeted drug in guideline, more drugs are now addressed in early phases of clinical trials and parts of them will be eventually approved.