In this study we have analysed 38 squamous cell carcinomas (SCC) two basal cell carcinomas (BCC), a malignant salivary gland carcinoma, a neurosarcoma and a Warthins carcinoma, all isolated from patients with head and neck cancers. These tumour types have been examined by PCR for loss of heterozygosity (LOH) on both arms of chromosome 17 using nine polymorphic microsatellite markers. LOH on 17p in SCCHN was found to be 50% (19/38), and often involved TP53 (42%) but more frequently involved the CHRNB1 locus (56%). Twelve tumours showed loss of heterozygosity on 17q (34%) and ten of these also had loss on 17p. Four SCCHN tumours lost an entire copy of chromosome 17. It was of particular note that 77% (10/13) of the SCCHN at the hypopharyngeal site had LOH at CHRNB1. We propose from our data that the 17p12-p11 region contains a novel predisposing gene for hypopharyngeal SCCHN that may function as a tumour suppressor gene.