One of the major problems with xenotransplantation is rejection of the tissue, which is caused by endogenous retroviruses within the donor's genome. For example, people who receive pig organs have to remain on immunosupressive therapy for the rest of their life because of the Porcine Endogenous RetroVirus (PERV)** present in the pig organ tissue. Endogenous retroviruses have also been found in cats, birds (especially chickens), mice, fruit flies (Drosophila), baboons, and humans (which have several).

Scientists have worked on implicating endogenous retroviruses in such diseases as lupus, murine and feline leukemia, and human mammary tumors. They have also been implicated in resistance to HIV-1 and in adverse reactions to the MMR vaccine.

Approximately 99% of the human genome does not code for essential proteins. Most of this "junk DNA" codes for transposons or one of several various endogenous retroviruses, including the LINE elements, the SINE or Alu elements, and the HERVs. These can serve as valuable genetic markers as to locations of certain genes on certain chromosomes. They also seem to compose the vast majority of the DNA in centromeres.

** - great name, huh?