Because of their high efficiency, virus-based vectors are currently used in most gene therapy trials. Because such vectors bear some potential safety risks, nonviral expression systems could be an attractive alternative. Ideally, these vectors should be completely based on chromosomal elements and replicate as an autonomous unit in the recipient cell, thus avoiding the risk of insertional mutagenesis or immunological reactions of the recipient organism. Our limited knowledge of the epigenetic regulation of replication in mammalian cells does not yet allow the rational design of such constructs. But in the late 1990s it was shown that scaffold/matrix attached region (S/MAR)-based vectors can promote episomal replication and maintenance in mammalian cells. These vectors have found broad application in basic research but are now improved for their use in the safe and reproducible genetic modification of cells and organisms and in gene therapy.