Previous studies have suggested an association between alleles of the CYP27B1 (1-alpha hydroxylase) gene and autoimmune conditions. We have examined three single nucleotide polymorphisms (SNPs) that are located in the 5' region and promoter of the CYP27B1 gene for association in a cohort of Graves' disease and autoimmune Addison's disease subjects from the UK. Genomic DNA samples from white patients with autoimmune Addison's disease (n = 104) and healthy controls (n = 464) were genotyped by PCR-RFLP analysis for the SNPs at positions -1260 and -1077 5' of the coding CYP27B1 sequences. The -1260 SNP was also examined in a cohort of patients with Graves' disease (n = 446). Chi 2 testing of contingency tables was used to determine the significance of genotypes and alleles. Haplotype frequencies and linkage disequilibrium measures were estimated using the UNPHASED and HAPLOVIEW packages. Alleles at the three CYP27B1 markers were in tight linkage disequilibrium with each other and all showed association with autoimmune Addison's disease. The maximum evidence for association was with the -1260 C allele (76.0% in Addison's subjects versus 64.9% in controls; P = 0.003; odds ratio 1.71 (5-95% confidence intervals, 1.20-2.44). A global test of significance for the common -1918 T, -1260 C and -1077 G haplotype was significant in Addison's subjects compared with controls (P = 0.01). In contrast, there was no association of alleles at the -1260 SNP with Graves' disease. We are able to confirm that a CYP27B1 promoter allele is associated with autoimmune Addison's disease, and extend this finding to include an associated promoter haplotype.