Like any disease treatment, gene therapy should be safe and efficacious. Safety can be addressed by directly correcting the defective gene itself or by ensuring that genomic integration of a transgene is site-specific. Unfortunately, it has proven difficult to achieve this level of safety without a concomitant loss in efficiency of gene correction or insertion. In this review, recent research attempts to achieve efficient site-specific gene therapy, including strategies using targeted gene conversion, adeno-associated virus vectors and site-specific bacteriophage recombinases are discussed. We believe that these approaches hold promise for site-specific, safe and efficient gene therapy.