Desmosomal junctions are specialized structures critical to cellular adhesion within epithelial tissues. Disassembly of these junctions is seen consequent to the development of autoantibodies directed at specific desmosomal proteins in blistering skin diseases such as pemphigus. However, many details regarding cell junction activity under normal physiological and disease conditions remain to be elucidated. Because of their complex structure, desmosomal junctions are not well suited to existing techniques for high-resolution three-dimensional structure-function analyses. Here, atomic force microscopy (AFM) is used for detailed characterization and visualization of the cell junctions of human epithelial cells. We demonstrate the ability to image the detailed three-dimensional structure of the cell junction at high magnification. In addition, the effect of specific antibody binding to desmosomal components of the cell junction is studied in longitudinal analyses before and after antibody treatment. We show that antibodies directed against desmoglein 3 (a major component of the desmosomal structural unit, and the major target of autoantibodies in patients with pemphigus vulgaris) are associated with changes at the cell surface of the human keratinocytes and alterations within keratinocyte intercellular adhesion structures, supporting the assertion that cell structures and junctions are modified by antibody binding. The present study indicates that the molecular structure of gap junctions can be more completely analyzed and characterized by AFM, offering a new technological approach to facilitate a better understanding of disease mechanisms and potentially monitor therapeutic strategies in blistering skin diseases. From the Clinical Editor Disassembly of desmosomal junctions is seen in blistering skin diseases such as Pemphigus. This present study demonstrates that the molecular structure of gap junctions can be more completely analyzed and characterized by atomic force microscopy.