BACKGROUND Pemphigus vulgaris (PV) and pemphigus foliaceus (PF) are autoimmune blistering diseases characterized by loss of cell-cell adhesion and by autoantibodies directed against epidermal cadherins. The ultrastructural localization of PV antigen remains controversial, whereas the location of PF antigen seems to be established. The use of different techniques could explain these various data. To investigate this matter, indirect immunoelectron microscopy (IEM) and Western blot analysis on bovine tongue epithelium were used. METHODS Serum samples from patients with PF(3), PV (4) and control samples from healthy patients (2) were analysed in this study. The inclusion criteria were based upon characteristic clinical features, level of epidermal cleavage on histological preparations and presence of circulating anti-epithelial cell surface antibodies. Indirect IME was performed on normal human skin. Peroxidase labelling was used. Serum samples were also analysed by western immunoblotting on bovine tongue epithelium. RESULTS Indirect IEM examination of PV sera showed immune deposits located both on desmosomal and extra-desmosomal areas, whereas in PF, IgG deposits were strictly localized on desmosomal structures. By Western blot analysis, PV sera recognized a 130 kDa polypeptide and PF sera a 150 kDa polypeptide. CONCLUSIONS Indirect IEM on normal human skin using peroxidase labelling was used because of the best antigenic conservation obtained. Our results suggest that PV antigen could exist both on desmosomal junctions and adherens junctions, whereas PF antigen (desmoglein I) is restricted to desmosome.