It is not well known that the correlation between HLA antigens and response to cancer therapy. To evaluate the correlation among patients' outcome, HLA antigens and therapies, we used the hierarchical clustering analysis (Ward method). We examined HLA antigens as biomarkers as well as models of gene polymorphism in 1753 gastric cancer patients followed over 25 years after treatment. Among these patients, we identified that HLA haplotypes; HLA-B54-Cw1-DQ4-DR4, might be restricting to Fluoropyrimidine drugs plus PSK therapy in gastric cancer. HLA haplotypes including HLA-B54 were candidate predictors for response to FPSK therapy in gastric cancer. HLAs will be useful biomarkers for response to therapy in Japanese patients.