Cells traffic in both directions between the fetus and the mother during pregnancy. Recent studies indicate that a low level of fetal cells commonly persists in the maternal circulation for years after pregnancy completion. The harboring of DNA or cells from another individual at low levels is called microchimerism. Chronic graft-vs-host disease is a condition of human chimerism that shares similarities to some autoimmune diseases and for which the specific HLA genes of donor and host are known to be of central importance. Considered together with the female predilection to autoimmunity, these observations led to the hypothesis that microchimerism and HLA genes of host and non-host cells are involved in autoimmune disease. The hypothesis also extends to men and females who have not been pregnant because there are other sources of microchimerism. Maternal cells are now know to persist in her progeny and microchimerism can also derive from a twin or from a blood transfusion. Studies of systemic sclerosis, primary biliary cirrhosis, Sjögrens syndrome, polymorpyhic eruption of pregnancy, myositis and thyroid disease have both lent support and raised doubts about the role of microchimerism in autoimmune disease.