To gain a better understanding of the molecular changes in head and neck squamous cell carcinoma, we tested every autosomal arm of 29 primary head and neck tumors for allelic loss. Fifty-eight microsatellite markers were used with at least two-thirds of patients informative for each chromosomal arm tested. A high frequency of allelic loss was found on chromosome 9p where 21 of 29 (72%) tumors had loss of heterozygosity for at least one polymorphic marker on this arm. Chromosomes 3, 11q, 13q, and 17p exhibited loss in over 50% of all informative cases, while chromosomes 4, 6p, 8, 14q, and 19q displayed loss in greater than 35% of all cases tested. Additionally, several other chromosomal arms exhibited loss of heterozygosity in 20 to 30% of tumors tested. This high frequency of allelic loss in these advanced stage neoplasms suggests multiple genetic steps in the progression of head and neck cancer and identifies several putative tumor suppressor loci on affected chromosomes.