We and others have shown that a family history of squamous cell carcinoma of the head and neck (SCCHN) is a risk factor for this disease. We performed a segregation analysis on a dataset comprised of 1429 first-degree relatives of 242 unselected cases of SCCHN and 934 first-degree relatives of 156 spouse controls. Using the SAGE software, we demonstrated that a Mendelian model was favored and a model postulating a purely environmental cause of SCCHN was rejected. The model suggests that 18% of the population who smoke and drink are susceptible. The lifetime risk for non-smokers and non-drinkers who are heterozygotes for the susceptible allele is close to zero, but for those heterozygotes who smoke and drink the risk is 14% by age 70. These findings suggest that specific genetic factors account for a significant fraction of the risk of SCCHN associated with a family history of SCCHN.