In drug development, major resources are invested into the development of cellular delivery systems to increase the effectiveness of a large array of potential therapeutics, such as proteins and oligonucleotides. These carriers comprise cell-penetrating peptides (CPPs), cationic lipids and cationic polymers. In recent years, evidence has been accumulating that these carriers not only act as mere pharmacokinetic modifiers but also interfere with cellular processes in various ways. In this review, we present an overview of the biological side effects associated with carrier systems. The focus will be on CPPs, which have been explored for a diverse set of cargos. Reported activities range from an induction of receptor internalization to the generation of reactive oxygen species. Ultimately, cell-penetrating molecules with such biological side effects might evolve into new bioactive agents that combine delivery capacity and pharmacophore in a single molecular entity. First examples for such molecules will be presented.