This paper presents the use of atomic force microscopy (AFM) to visualize and quantify the dynamics of epithelial cell junction interactions under physiological and pathophysiological conditions at the nanoscale. 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, these structures are complex and mechanically inhomogeneous, making it difficult to study and the mechanisms of autoantibody mediated keratinocyte disassembly remain largely unknown. Here, we have used AFM system to image and measure the mechanical property of living skin epithelial cells in culture. We demonstrate that the force measurement data can possibly distinguish the cell with different antibody treatment. Our demonstration of the use of AFM for in situ imaging and elasticity measurement positioned us to begin to investigate disease mechanisms and monitor therapeutic strategies in blistering skin diseases in much greater detail, to meet the demands for understanding disease pathology at the local, or tissue level.