The revolutionary evolution in science and technology has made it possible to face adequately three main challenges in modern medicine: old diseases changing, new diseases appearing, diseases remaining unknown. In this paper we review the road travelled by the pathologist in search of a method which is based upon the application to routine work of instruments and techniques which once were available for research only. Application to tissue studies of immunological and molecular biology techniques allows a dynamic interpretation of biological phenomena with special regard to gene regulation and expression. The method implies stepwise investigations, including immunohistochemistry, EM and in situ hybridization, in order to progress from the suggestive features detectable in routinely stained preparations to more characteristic, specific and, finally, pathognomonic features. HE-stained preparations and appropriate immunohistochemical stains enable recognition of phenotypic changes which may reflect genotypic alterations. Thus there is a logical and methodological link between the simple HE and the most powerful techniques so far introduced in pathology: immunohistochemistry and in situ hybridization.