In the past decade, the synthesis of nanostructures of various geometries, chemical and physical behaviour has been intensively developed not only for its fundamental scientific interest but also for many technological, biosensing and medical applications, such as contrast increase of MRI, in bioaffinity assays, and targeted drug delivery. These structures have also unusual optical, electrical and catalytic properties, which allow for their potential and exciting applications in the above areas. In this respect I will focus on two types of representatives of such structures: magnetic nanoparticles and hollow polymeric nanocapsules. For the first type of nanostructures, I will discuss on the attachment of molecular adlayers to the surface of various types of nanoferrites for the purpose of their stabilisation, changing the hydrophilic/hydrophobic balance or to provide their surface with suitable functional groups ready for further modifications and tailoring, e.g., for targeted drug delivery. For the case of the second type of nanostructures, a considerable stress is laid on synthesis and characterization of hollow polymeric structures in which different molecules or particles can be entrapped or encapsulated. We have recently developed several new methods of preparation of polymeric micro- and nanocapsules using gaseous, liquid or solid particles that template growth of 3D structures The role of such capsule is to provide proper environment for molecules and nanoparticles and to protect them from degradation when they travel through the tissues to the targeted site. Moreover, the capsules allow much higher loading densities of the drug molecules when compared to e.g., covalent grafting on nanoparticle surface. Additionally, polymer shells influence the antifouling characteristics of the nanoparticles and also contribute to their effective hydrodynamic size, one of the key factor in avoiding the response by the ReticuloEndothelial System (RES).