We have previously identified a set of genes associated with hypothyroid disease in a region of the genome that is rich in immune genes. We have now performed a whole genome scan comparing 58 Rhodesian Ridgebacks, Doberman and Boxers having hypothyroid disease with 100 unaffected control dogs, which has revealed 210 SNPs that are significantly associated with hypothyroid disease. Thirty one of these SNP associations are highly significant and give us great hope that we will be able to identify other genes/loci associated with this disease. If we can identify such genes, it may be possible to start selective breeding to reduce the risk of Rhodesian Ridgebacks, Doberman, Boxers and other breeds developing hypothyroid disease.