The article is devoted to the identification of methodological possibilities of synergetics (in particular, “a whole in a whole” concept) in research of the results of the interaction of nano- and bio-objects («nanomaterial-biological object” systems) based on their self-organizing nature. The authors are moving from a discrete examination of objects of a synergistic order (on the one hand, a human body, on the other hand, nanoparticles) towards the comprehension of wider systems — nanobiocomplexes. The emphasis on the relevance of the holistic (against the background of the set-theoretic) approach in the study of a complex whole is made, the synergetic principles of its construction are shown.