This review has summarized the currently available literary information on the possibilities of applying the electron microscopy (EM) in experimental, clinical medicine and in related scientific fields. Concrete results that highlight the role of using EM in highly specialized clinical practice, where ultrastructural studies both complement routine light-optical methods and are their alternative has been presented. Examples of relevant data on virology, toxicology, nephrology, ophthalmology, neuropharmacology, forensic medicine, military and reproductive medicine have been provided. In a number of cases, the results achieved by EM were unique and capable of accurately describing the typical features of certain organs and cells. EM methods are indispensable for identifying, clarifying and recognizing various rare combined defects and pathologies, as well as for investigating the pathogenesis of viral infections and the mechanism of action of drugs.