The characterization of autoantibody specificities in rheumatic diseases and other disorders is important for both diagnostic and basic research purposes. The epitopes of autoantigens recognized by autoantibodies have been extensively investigated. Epitopes may range in complexity from simple linear sequences of amino acids to conformational structures composed of multiple components. In addition to this structural complexity, the frequency with which an autoantigen and its epitopes are recognized in a patient population would be useful in diagnosis and in defining disease subgroups, and could provide information about the disease prognosis. In this review, the epitope mapping of autoantigens, and the types of autoepitopes are introduced using examples most of which we clarified experimentally.