Karyotyping and polymorphisms within the DCC (deleted in colon cancer) locus (18q21) were used to analyze loss of chromosome 18 in squamous cell carcinomas (SCC). Tumors from 26 patients (including 7 for whom matched tumor and normal DNA samples were available) were examined for heterozygosity within DCC. Of the seven normal-tumor combinations, four were informative. Two of these had loss of heterozygosity (LOH) at DCC. For 19 SCC tumor cultures normal tissue was not available. These were scored only as homozygous or heterozygous. The majority were homozygous. Only 3/19 (15%) were heterozygous. In contrast, in a panel of normal blood samples the majority, 11/16 (69%), were heterozygous. Allelic zygosity was concordant with the chromosome 18 content in the 16 tumors that were also karyotyped. Tumors from 40 patients, 37 that were karyotyped and three that were informative at the DCC locus, were assessed for loss of chromosome 18 and patient survival. Loss of part or all of chromosome 18 occurred in tumors from 25. Twenty-seven of the 40 patients have died and 13 are alive. There was strong association between loss of 18 and overall survival. Of those who are alive only 5/13 (38%) had loss of 18, whereas among those who have died 20/27 (74%) had loss of 18. By chi 2 analysis the association of loss of 18 and death from cancer was significant (p > 0.01). The high frequency of chromosome 18 loss in SCC suggests that this region contains one or more tumor suppressor genes important in the clinical behavior of SCC. DCC is one candidate, but other regions of loss not including the DCC locus indicate that chromosome 18 probably contains more than one tumor suppressor locus. Prospective studies of chromosome 18 loss as a single prognostic indicator are strongly indicated in this tumor type since loss in early stage tumors might indicate a need for more aggressive therapy than would be given on the basis of staging alone.