The manufacture of 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 use of engineered chromosomes has been considered. To date, the most successful technique has been based on the artificial chromosome expression or ACE System, which consists of the targeted transfection of cells containing mammalian based artificial chromosomes with multiple recombination acceptor sites. This ACE System allows for the specific transfection of single or multiple gene copies and eliminates the need for random integration into native host chromosomes. The utility of using artificial engineered mammalian chromosomes, specifically the ACE System, is illustrated in several case studies covering the generation of CHO cell lines expressing monoclonal antibodies.