Abstract: A novel nucleotide sequence integration and targeting system is described. The system employs adeno-associated virus (AAV) derived vectors which include a selected nucleotide sequence bounded by AAV inverted terminal repeats (ITRs). An AAV rep coding region is also provided, enabling the targeted integration of the selected nucleotide sequence into the genome of a suitable target cell. The nucleotide sequence integration system of the present invention can deliver and integrate large segments of DNA into the genome of target cells. Further, the subject integration system provides the advantage of site-specific integration of the selected nucleotide sequences in a target cell genome, thereby avoiding insertional mutagenesis events experienced with prior systems.