Although assays to detect thyroid autoantibodies have been available for more than 40 years, their place in the clinical management of thyroid disease has remained controversial; however, novel automated detection techniques using recombinant antigens are increasing the sensitivity and specificity of the assays, particularly for antibodies to the TSH receptor. In addition, new antigenic targets have been defined including the sodium-iodide symporter and four eye muscle proteins targeted in Graves' ophthalmopathy. This article summarizes the immunobiology, assay methodology and prevalence in thyroid diseases of each of the major thyroid autoantibodies before discussing the clinical indications for their use in thyroid diseases.