Tylosis is a benign autosomal dominantly inherited disorder of the skin that manifests as focal thickening of the palmar and plantar surfaces. The disorder is associated with the early onset of squamous cell oesophageal cancer in two large families from the UK and US and a smaller German pedigree. The familial cancer association is rare in the general population, but the gene is also implicated in the development of sporadic squamous cell oesophageal cancer. Previous work using the UK and US families has mapped the Tylosis with Oesophageal Cancer (TOC) gene locus to chromosome 17q25 between markers D17S785 and D17S722, spanning a region of approximately 500kb and containing at least 15 candidate genes. This region is covered entirely by 4 RPCI-11 BAC; 3 of which are now fully sequenced. Mutational analysis carried out on the coding regions of the candidate genes has not identified any disease-associated mutations. In this study, analysis of the sequence data revealed 20 novel microsatellites that ranged from di- to penta-nucleotide repeats. Initial haplotype studies on members of the UK and US pedigrees showed that 9 of the repeats were polymorphic in the TOC families. Two of the new markers, D17S2239 and D17S2244 delineated crossover events in 2 UK family members that reduced the minimal region from ~500kb to ~65kb. This not only removed 13 candidate genes from the study but has also eliminated 3 of the BAC clones from the minimal contig. A bioinformatical analysis of this 65kb region using several gene prediction programs revealed a previously uncharacterised gene (JEL). Mutation analysis of the coding regions of this gene did not reveal any TOC specific mutations. A collaboration with the Wellcome Trust Sanger Institute in Cambridge UK, enabled the entire non-repetitive portion of the ~65kb sequence to be sequenced in four TOC family members (an affected and unaffected member from each of the UK and US families). This analysis identified 58 single nucleotide polymorphisms (SNPs) in one or both of these families, 52 of which were previously undescribed. Further fine mapping of the TOC disease locus by haplotype analysis of 23/58 SNPs allowed the reduction of the minimal region to ~42.5kb. A novel minisatellite and a deletion/insertion were also found that demonstrated possible differences between the affected and unaffected individuals in both families and these findings require further investigation. A variety of techniques including both bioinformatical methods and practical procedures have been used in this study to identify the candidate genes within the TOC minimal region. Bioinformatic programs were used to predict gene structures and coding regions within the contig sequence data, whereas practical methods such as RT-PCR were used to confirm that the genes were expressed. The overall results identified STAP/Cytoglobin as the major candidate for the TOC gene. Several disease- specific lesions have also been identified but require further investigation to determine the exact function of their action.