Antibiotics are agents that kill or inhibit bacterial growth when added to the growth media. In order to selectively grow bacteria carrying a specific plasmid, genes are integrated on the plasmid that convey a resistance against a certain agent. As in this scenario, the plasmid provides a benefit, the resistance gene ensures that the plasmid persist within the bacterial population. However, the use of antibiotics and antibiotic resistance genes bears certain risks. Horizontal gene transfer may lead to broader distribution of the antibiotic resistance or, depending on the application, the resistance gene might also be transferred into the patient’s genome. Thus, alternative selection systems or strategies will become more important in near future. In its guidelines for medical gene transfer products, the European Medicines Agency (EMA; formerly European Agency for the Evaluation of Medicinal Products, EMEA) recommends abandoning the use of selection markers, such as resistance to antibiotics, in plasmid DNA products (CPMP/BWP/3088/99). In the interest of increased safety, national bodies (e.g. Paul-Ehrlich-Institut in Germany; AFSSAPS in France; and MCA in the United Kingdom) have adopted this recommendation. In reaction, PlasmidFactory has developed a method for the reliable large-scale production of Minicircle DNA. This already meet future’s regulations due to the lack of selection markers.