The dermal-epidermal junction contains a network of structural proteins that link epidermis and dermis. A central component of this complex is the cell membrane-associated hemidesmosomal plaque. Formation of autoantibodies against different components of this hemidesmosomal anchoring complex can lead to subepidermal blisters. Such autoantibodies have been frequently used to characterize the target antigens at the molecular level. Autoimmune subepidermal blistering diseases include bullous pemphigoid, pemphigoid gestationis, lichen planus pemphigoides, linear IgA disease, cicatricial pemphigoid, anti-p450-, anti-p200- and anti-p105-pemphigoid, epidermolysis bullosa acquisita, bullous systemic lupus erythematosus and dermatitis herpetiformis Duhring. Differences in the clinical picture of these diseases can be attributed, at least in part, to the different specificity of the autoantibodies involved. The autoimmune response is further modulated by inflammatory cells and other inflammatory mediators. Native and recombinant forms of the autoantigens are increasingly used for the diagnosis of these diseases.