The frequencies of HLA class I and II antigens and TNF-beta polymorphism in lung cancer patients were investigated in two areas with different immunogenetic backgrounds, in Okinawa and in mainland Japan (Honshu). In Okinawa frequencies of HLA-Cw3 in squamous cell lung carcinoma patients were higher and those of HLA-DR, both in all lung cancer and in adeno lung carcinoma patients, were lower compared to those of normal controls. Among serologic HLA-DR4-positive individuals, no difference of DRB1*04 gene allele frequency was shown between patients and controls. In Honshu no statistically significant difference of HLA-class I and II alleles frequencies was found; however, the frequency of TNF-beta 10.5-kb homozygote in lung cancer patients was lower than that of controls. For 2-year survival, there was no difference between DR4-positive and -negative individuals and also between each TNF-beta type in Okinawa. In contrast, Honshu patients with 10.5-kb homozygote showed an improved 5-year survival ratio compared to those with heterozygote. We postulate that different immunogenetic backgrounds or environments might have caused the varying HLA or TNF-beta association in the predisposition to or prognosis of lung cancer.