Starting in the 1960ies, with a common availability of high resolution microscopes and the introduction of negative staining and ultrathin sectioning of microwave embedded infectious tissues, pathogen diagnosis on basis of electron microscopy (EM) has become increasingly important. An EM-based lab diagnosis turned out to be useful in a wide spectrum of indications like “rapid diagnosis in emerging diseases”, “search for otherwise undetectable agents” (“open view”), the need for “catch-all-methods” and/or “rapid differential diagnosis”. Since then, the use of transmission electron microscopy, and to a lesser extent scanning electron microscopy provide a multiplex platform for the detection and differentiation of a wide range of pathogens (Fig. 1-3). Examples will be given. In past, EM was involved with the detection and identification of broad range of viruses some of which have impacted on human, veterinary and wildlife health. Many of the diseases caused by viruses have emerged from anthropogenic based perturbations of the environment including altered habitat e.g. changes in the number of vector breeding sites and/or host reservoirs, niche invasions, changes in biodiversity, genetic changes of disease vectors or pathogens, and environmental contamination of infectious agents.

However, the use of diagnostic EM declines radically since the late decade of the 20th century which was characterized by a continuous shifting of research interests to molecular biology. With whole genome sequencing some of the indications mentioned above like “catch-all-method” or “search for undetectable pathogens – open view” seem to be on first sight no longer existing. Is it now a change of paradigm, a still going onward decline or may diagnostic EM play still an essential role in pathogen diagnosis? The future of diagnostic EM, its constraints and its welfare for the society is discussed. Be aware, since September 11^th executive authorities have noticed that molecular biology and EM complement each other and most modern diagnostic centres of disease control still execute both techniques in their diagnostic programme; but for how long?. Additionally increased mobility, changes in life style, global trade and social unrest are supporting the spread of emerging or re-emerging infections. Anyway, we should be aware that molecular biology of today with whole genome sequencing as well as electron microscopy bear a lot of uncertainties in their technical procedure – technical sources of error which should be always be in mind during diagnostic procedure.

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