Hypothyroidism represents a significant clinical problem in dogs, but definitive diagnosis remains difficult. Canine hypothyroidism is considered to be an autoimmune disease, based on its clinical and histological similarities to Hashimoto’s thyroiditis in man (Beierwaltes and Nishiyama 1968), and because of the presence of autoantibodies to thyroglobulin (Mizejewski et al. 1971). Immune-mediated conditions are likely to have a genetic component to their aetiology and this is supported by the fact that many such diseases display increased breed predilection or resistance. Breeds predisposed to hypothyroidism include Doberman Pinschers and Golden Retrievers, Poodles, Boxers, and Dachshunds (Happ 1995; Nachreiner et al. 2002; Panciera 1994). We have previously identified associations with the canine MHC in dogs (Kennedy et al. 2006a; Kennedy et al. 2006b), in Doberman Pinschers, English Setters, and Rhodesian Ridgebacks, as well as a larger cohort including many different breeds. We now wish to collect further samples primarily from other dog breeds to establish a second cohort in which to confirm the results of our previous studies.