An individual difference in the susceptibility to chemical carcinogens is one of the most important factors in the estimate of risk of human cancer. Recently, it has been reported that genetic risk for tobacco-related cancers is associated with polymorphisms of the CYP1A1 and GSTM1 genes in terms of genotype frequencies and cigarette smoking dose. In this study, we investigated the inter-individual difference in genetically determined susceptibility to oral squamous cell carcinoma (SCC) in relation to cigarette smoking dose in a Japanese population. DNA samples were obtained from both patients and controls. We identified individuals at high risk genetically for oral SCC in terms of polymorphisms of the CYP1A1 and GSTM1 genes. This study then compared the estimated total number of cigarettes smoked by patients with those smoked by controls. In this case-control study, we estimated the odds ratios of susceptible to non-susceptible individuals. CYP1A1 genotype C and GSTM1 deficiency were frequently found among oral SCC patients. Patients with genotype C and GSTM1 deficiency contracted carcinoma after fewer cigarettes than those with other genotypes. Individuals with these two genotypes were at remarkably high risk at a low dose level of cigarette smoking. Individual differences in polymorphisms of the CYP1A1 and GSTM1 genes is one important factor in the estimate of risk of oral SCC at a low dose level of cigarette smoking.