Xenotransplantation, the transfer of cells, tissues or organs between species, has the potential to overcome the critical need for organs to treat patients. One major barrier in the widespread application of xenotransplantation in the clinic is the overwhelming rejection response that occurs when non-human organs encounter the human immune system. Recent progress in developing new and better genome engineering tools now allows the genetic engineering of genes and pathways in non-human animals to overcome the human rejection response and provide an unlimited supply of rejection-free organs. In this review, the benefits and drawbacks of various genome engineering protocols, and examples of their application in xenotransplantation, are discussed.