All the nanotechnological devices designed for medical purposes have to deal with the common requirement of facing the complexity of a living organism. Therefore, the development of these nanoconstructs must involve the study of their structural and functional interactions and the effects on cells, tissues, and organs, to ensure both effectiveness and safety. To this aim, imaging techniques proved to be extremely valuable not only to visualize the nanoparticles in the biological environment but also to detect the morphological and molecular modifications they have induced. In particular, histochemistry is a long-established science able to provide molecular information on cell and tissue components in situ, bringing together the potential of biomolecular analysis and imaging. The present review article aims at offering an overview of the various histochemical techniques used to explore the impact of novel nanoproducts as therapeutic, reconstructive and diagnostic tools on biological systems. It is evident that histochemistry has been playing a leading role in nanomedical research, being largely applied to single cells, tissue slices and even living animals.