The HLA and CTLA-4 gene regions, on chromosomes 6p21 and 2q33 respectively, have been consistently associated with Graves' disease (GD). Recent data indicate that both DRB1 (in the HLA class II region) and the 3' untranslated region of the CTLA-4 gene are the most likely regions harbouring the aetiological variants for susceptibility to GD. It is not known, however, whether these variants lead to expression of specific sub-phenotypes in subjects with GD, or contribute to disease susceptibility within specific population groups e.g. females or those of young age. Using a dataset of 880 GD patients genotyped at the DRB1 and CT60 (the most strongly associated single nucleotide polymorphism at CTLA-4) loci, we performed multiple logistic regression analysis to determine (i) whether these loci contributed to phenotype in those with GD (goitre size, presence of ophthalmopathy and biochemical severity indicated by free T4 at presentation), and (ii) whether through interaction with each other, age or gender, susceptibility to GD was increased. No association was observed between DRB1 or CT60 genotypes and GD phenotypes or gender respectively. Association was observed between DRB1 and age of onset of disease (p=0.0041), where DRB1*03 homozygous patients had an average age of onset 12.9 years younger than DRB1*07 homozygotes (p=0.036). In a case-only test of interaction, CT60 genotype (GG) plus female gender predicted disease risk (p=0.0097). Similarly, interaction was observed between DRB1 and CT60, where the initial odds ratio parameter estimate of developing GD for a DRB1*03 homozygote was 5.04, which decreased through CT60 genotypes GG, GA and AA to 0.176. We therefore concluded that the two most important genetic loci in determining GD susceptibility, namely HLA-DRB1 and CT60, interact with one another such that individuals at greatest risk of developing GD are young females, who are homozygous for both the DRB1*03 and CT60 G alleles.