One of the most promising strategies to improve the bioavailability of active pharmaceutical ingredients is based on the association of the drug with colloidal carriers, for example, polymeric nanoparticles, which are stable in biological environment, protective for encapsulated substances and able to modulate physicochemical characteristics, drug release and biological behaviour. The synthetic polymers possess unique properties due to their chemical structure. Some of them are characterized with mucoadhesiveness; another can facilitate the penetration through mucous layers; or to be stimuli responsive, providing controlled drug release at the target organ, tissues or cells; and all of them are biocompatible and versatile. These are suitable vehicles of nucleic acids, oligonucleotides, DNA, peptides and proteins. This chapter aims to look at the 'hot spots' in the design of synthetic polymer nanoparticles as an intelligent drug delivery system in terms of biopharmaceutical challenges and in relation to the route of their administration: the non-invasive-oral, transdermal, transmucosal (nasal, buccal/sublingual, vaginal, rectal and ocular) and inhalation routes-and the invasive parenteral route.