The biomedical applications of iron oxide nanoparticle clusters (FeO NPCs) are particularly dependent on the ability to control cluster size, architecture and surface composition, as these properties largely determine biodistribution and the extent of contrast enhancement. This highlights the need for methods to assembly FeO NPs into assemblies of controlled size. Our group recently developed a method for producing stable NPC suspensions with good control over the size by a novel process, competitive stabilizer desorption. CSD allows production of stable CHCl3 suspensions of monodisperse, oleic acid stabilized, NPCs with sizes ranging from 40–500 nm. In CSD a substrate competes with the NP surface for the stabilizing oleic acid ligand, resulting in destabilization of NP suspensions by the gradual removal of the surface ligand. In the first part the optimization of an improved version of CSD using a CHCl3:H2O interface as the competitive substrate, is reported. The details of the mechanistic study that permitted the scale-up are presented in detail. The robust CSD process has been applied to the assembly of different types of NPs and combinations of more than one NP type (including FeO and metal ferrite NPs), different types of substrates, NP size and finally in presence of external solicitation such as magnetic field. The development of a novel flow set-up that ideally allows the production of large quantities of NPC is also presented. The second part of the thesis presents novel methods for the transfer of nanoparticle assemblies from organic to aqueous media has been also developed which can be used to transfer clusters of controlled size in large quantities. It is shown that the final NPCs have good colloidal stability and very narrow size distributions. Assessment over the biotoxicity of these materials was also undertaken in order to study their behavior in biological systems.