Transmission electron microscopy (TEM) has long been the best available method for the diagnosis of epidermolysis bullosa. Today, TEM is largely superseded by immunofluorescence microscopy mapping, which is generally more available. This article discusses its continuing role in confirming or refining results obtained by other methods, or in establishing the diagnosis where other techniques have been unsuitable or have failed. It covers key steps for optimizing tissue preparation, features of analysis, recently classified epidermolysis bullosa disorders, and strengths and weaknesses of TEM.