In this work we describe a design of multifunctional complexes based on magnetic nanoparticles and anti-cancer mini-antibodies of scFv format that selectively recognize oncomarker HER2/neu on the surface of human breast adenocarcinoma cells. ScFv, having small size and being fully genetically encoded, offer significant advantages over full size antibody for targeted delivery of nanoparticles both in vitro and in vivo, such as low cross-reactivity and immunogenicity and ease of biotechnological production in prokaryotic expression systems. These structures were obtained through the use of the barnase, barstar protein pair as a molecular glue between nanoparticles and recognizing antibodies. Moreover, for demonstrating the ability of obtaining a high diversity of scFv and magnetic nanoparticles-based constructions, we obtained complexes of magnetic nanoparticles and fusion protein of anti-HER2/neu mini-antibody 4D5scFv and fluorescent protein mCherry that specifically stained HER2/neu positive cells. Application of such targeted nanoparticles opens up new possibilities for designing new effective methods of cancer diagnostics.