Autoimmune liver disease and thyroid disease. Autoimmune disorders, including autoimmune thyroid disorders, occur in up to 34% of patients with autoimmune hepatitis. The presence of these disorders is associated with female sex, older age and certain human leukocyte antigens (HLAs).he liver might also be affected in patients with the genetic autoimmune disease, polyglandular autoimmune syndrome, which affects the thyroid gland. This interaction again demonstrates crosstalk between autoimmune disturbances in the thyroid system and the liver.