The synthesis of superparamagnetic nanostructures, especially iron-oxide based nanoparticles (IONPs), with appropriate surface functional groups has been intensively researched for many high-technological applications, including high density data storage, biosensing and biomedicine. In medicine, IONPs are nowadays widely used as contrast agents for magnetic resonance imaging (MRI), in hyperthermia therapy, but are also exploited for drug and gene delivery, detoxification of biological fluids or immunoassays, as they are relatively non-toxic. The use of magnetic particles in vivo requires IONPs to have high magnetization values, diameters below 100 nm with overall narrow size distribution and long time stability in biological fluids. Due to the high surface energies of IONPs agglomeration over time is often encountered. It is thus of prime importance to modify their surface to prevent aggregation and to limit non-specific adsorption of biomolecules onto their surface. Such chemical modifications result in IONPs being well-dispersed and biocompatible, and allow for targeted delivery and specific interactions. The chemical nature of IONPs thus determines not only the overall size of the colloid, but also plays a significant role for in vivo and in vitro applications. This review discusses the different concepts currently used for the surface functionalization and coating of iron oxide nanoparticles. The diverse strategies for the covalent linking of drugs, proteins, enzymes, antibodies, and nucleotides will be discussed and the chemically relevant steps will be explained in detail.