The application of molecular techniques to the study of human pregnancy has resulted in knowledge that the placenta is only a relative barrier to traffic of fetal and maternal cells. Moreover, long-term persistence of fetal cells in the maternal circulation and maternal cells in her progeny have been described. Harboring of cells from another individual is referred to as chimerism and microchimerism indicates low levels of non-host cells. The clinical features of a known condition of human chimerism, chronic graft-versus-host disease that occurs after stem cell transplantation, resemble spontaneously occurring autoimmune diseases including systemic sclerosis, Sjögren's syndrome, primary biliary cirrhosis, and sometimes myositis and systemic lupus. A critical determinant of chronic graft-versus-host disease is the HLA relationship of donor and host cells. When considered together, these observations have led to a new area of research investigating whether microchimerism and HLA-relationships are involved in the pathogenesis of some autoimmune diseases.