Pemphigus vulgaris is an autoimmune bullous disorder characterized by autoantibodies directed against desmoglein 3. A group of 19 pemphigus vulgaris sera were characterized by immunoblotting, immunofluorescence, immunoprecipitation, and the passive transfer mouse model. The aim of these studies was to determine the specificity of the autoantibody response in these patients. All patients had clinical and histologic evidence of pemphigus vulgaris. Fogo selvagem sera (n = 8), bullous pemphigoid sera (n = 8), antinuclear antibodies positive sera from patients with lupus erythematosus (n = 2), and normal human sera (n = 8) were used as controls. All pemphigus vulgaris patients showed titers of IgG autoantibodies by indirect immunofluorescence ≥1:160, predominantly of the IgG4 subclass and immunoprecipitated recombinant desmoglein 3 expressed in the baculo-virus system. Patients with disease localized to the mucous membranes showed no reactivity with desmoglein 1 and only one had weak reactivity with mouse skin by indirect immunofluorescence (titer = 1:20). Sera of four of these mucosal patients were tested in the mouse model and three of four did not elicit skin or mucosal disease in the animals. In contrast, sera from all seven patients with disease involving the skin and mucous membranes (generalized disease) produced disease in neonatal mice. In one patient the disease evolved from pure mucosal involvement associated with anti-desmoglein 3 antibodies to a disorder involving mucosas and skin. This transition was associated with the appearance of anti-desmoglein 1 antibodies in the patient's serum. These studies indicate that the autoantibody response in pemphigus vulgaris is heterogeneous. Epitopes recognized by some pemphigus vulgaris sera are species specific and others maybe mucosal specific.