Although electron microscopy no longer enjoys the important role in the diagnosis of interstitial lung diseases that it had in the 1960s and 1970s, it remains an important adjunct in the differential diagnosis of certain pulmonary diseases. Examples include various manifestations of systemic lupus erythematous pneumonitis, in which the presence of tubuloreticular structures and electron-dense deposits are useful for diagnosis; immotile cilia disorders, in which qualitative and now quantitative studies of the cilia of respiratory epithelial cells can help to establish the diagnosis; infections by viruses and other subcellular microorganisms as shown by the role played by electron microscopy in the initial diagnosis of the Hantavirus pulmonary syndrome; pneumoconioses, in which, in conjunction with elemental analysis probes, scanning electron microscopy is of critical importance in establishing the presence of offending foreign compounds in lung tissue or fluids; pulmonary fibrilloses, such as amyloidosis, light chain disease, and fibrillary glomerulonephritis, affecting the lung; and cases of alveolar proteinosis or Langerhans cell granulomatosis diagnosed from fluids such as bronchoalveolar lavages or small tissue samples. As important, electron microscopy remains of enormous usefulness in the study of early structural events leading to the pathogenesis of diseases. For example, recent uses of the technique have focused on the alveolar-capillary wall damage induced by alveolitis in hypersensitivity pneumonitis and sarcoidosis. In summary, electron microscopy remains a useful method in the study and diagnosis of some interstitial lung diseases, but because of its expense it is incumbent on the clinician to use good judgment in the selection of cases and diseases for study by this method.