Single-nucleotide polymorphisms (SNPs) within the tumour necrosis factor alpha (TNF-alpha) gene on chromosome 6p21.3 have been associated with many autoimmune diseases; however, results have been conflicting and accurate allele frequencies have never been established in a UK Caucasian population. The aim of this study was to assess the frequency of 22 known TNF-alpha SNPs in a UK Caucasian control population and investigate association of all polymorphisms with >5% minor allele frequency in a large case-control data set of patients with Graves' disease (GD). Eight of the 22 SNPs had minor allele frequencies >5% and were investigated further. The other 14 SNPs were present in the UK population at frequencies ranging from 0 to 4.7%. A significant increase of the A allele of the -238 SNP was seen in GD patients when compared with control subjects (9.6 vs 6.8%, respectively; P=0.003) and mirrored in the genotype distribution (P=0.009). Furthermore, association of the -238 SNP appears not to be due to linkage disequilibrium of the known HLA-DRB1(*)03 associations with GD. This study has established accurate allele frequencies of TNF-alpha SNPs in a UK population and provides preliminary evidence for association of the TNF-alpha gene with GD.