Patients with head and neck cancers have a high (2-3%/year) incidence of second primary lesions. Clinically, these new lesions are identified either simultaneously with the primary lesion (synchronous) or after a period of time (metachronous). This observation has been attributed to the concept of "field carcinogenesis," which is based on the hypothesis that prolonged exposure to carcinogens leads to the independent transformation of multiple epithelial cells at several sites. An alternative theory is based on the premise that any transforming event is rare; following initial transformation, the progeny of the transformed clone spread through the mucosa and give rise to geographically distinct but genetically related tumors. We analyzed the pattern of X-chromosome inactivation in multiple primary tumors from eight female patients with head and neck cancer. In addition, we used microsatellite analysis to examine the pattern of allelic loss on chromosomes 9p and 3p, identified as early events in the progression of head and neck malignancies. In four of four cases, multiple tumors demonstrated the same pattern of X-chromosome inactivation. In the remaining four cases, X-chromosome deletions prevented interpretation (n = 3), or the androgen receptor locus was noninformative (n = 1). In three of nine patients, multiple tumors displayed the same pattern of loss of heterozygosity, two with identical breakpoints on chromosome 9p. In one patient, there was an identical microsatellite alteration at a 3p locus, definitive evidence that these tumors arose from the same clone. Our findings suggest that in at least a proportion of patients with head and neck cancers, multiple primary tumors arise from a single clone.