We analyzed the location of binding sites for pemphigus vulgaris (PV) antigen and pemphigus foliaceus (PF) antigen in the human epidermis using serum samples obtained from three patients with PV and three patients with PF. Confocal laser scanning microscopy, immunofluorescent examination of ultrathin cryosections, and immunoperoxidase electron microscopy demonstrated discontinuous dots along the epidermal cell surfaces. Immunogold electron microscopy of ultrathin cryosections showed specific binding of PV and PF autoantibodies only to desmosomes. Post-embedding immunogold electron microscopy using cryofixation and cryosubstitution enabled the whole depth of the epidermis to be examined and the binding of PV and PF autoantibodies to be quantitated by counting gold particles. Both PV and PF autoantibodies bound to all desmosomes in the epidermis, but not to the surface of the non-desmosomal keratinocytes. The majority of auto-antibody binding occurred in the extracellular domain (PV, 62%; PF, 69%). The statistical analysis of two-way analysis of variance regarding the number of gold particles labeling a single desmosome confirmed a significant interaction between subtypes of pemphigus (PV and PF) and the different epidermal cell layers (p < 0.044). The results indicate that the number of gold particles bound to individual desmosomes with PV sera was significantly higher in the lower epidermis than in the upper epidermis, and that of PF sera showed reciprocal pattern. This inversely graded binding pattern suggests heterogeneity of the composition of the desmosomes, which may explain the differences in level of acantholysis between PV and PF.