Autoimmune disorders, for which hypothyroidism is one, have been cited by dog breeders as a concern. A diagnosis of hypothyroidism often accompanies other immune mediated diseases and many breeds are afflicted with several autoimmune disorders. This evidence suggests different autoimmune diseases actually reflect a common set of susceptibility genes that express differentially depending upon additional genetic mutations carried by an individual dog and response to environmental triggers. The twelve month acorn grant examined the entire canine genome using SNP microarrays to search for chromosomal regions associated with hypothyroidism in the Bearded Collie. No significant linkage was detected for any chromosomal region when evaluating either hypothyroidism contrasted with either hypoadrenocorticism alone or with dogs that had neither condition. However, when categorizing hypothyroid and hypoadrenocorticism dogs together as a generalized immune condition and looked for association with Bearded collies having neither disease, a 2.7 MB chromosomal region demonstrated significant association with the autoimmune status. We hypothesize that a set of susceptibility genes common to autoimmune disease exists within that region and we are planning on fine mapping this region.