Autophagy delivers protein aggregates, damaged organelles and intracellular microorganisms to the lysosome for degradation. The epidermis and other epithelia show significant levels of autophagy, however, the functions of autophagy in these tissues have remained elusive until recently. Here we review the experimental approaches for the investigation of autophagy in epithelia and discuss the roles of autophagy in epithelial cells with a focus on epidermal keratinocytes and thymic epithelial cells.