Manufacturing recombinant proteins at industrially relevant levels requires technologies that can engineer stable, high-expressing cell lines rapidly, reproducibly, and with relative ease. Commonly used methods incorporate transfection of mammalian cell lines with plasmid DNA containing the gene of interest. Identifying stable, high-expressing transfectants is normally laborious and time consuming. To improve this process, the ACE System has been developed based on pre-engineered artificial chromosomes with multiple recombination acceptor sites. This system allows targeted integration of single or multiple gene copies and eliminates the need for random integration into native host chromosomes. To illustrate the usefulness of the ACE System in generating stable, high-expressing cell lines, we present several case studies covering CHO cell lines expressing monoclonal antibodies.