It is now well recognized that cells traffic in both directions between fetus and mother during pregnancy. Moreover, fetal cells have been found to persist for years, probably for a lifetime, in the circulation of healthy women. Harboring of cells from another individual at low levels is called microchimerism. Women have a predilection to autoimmune disease, and chronic graft-versus-host disease, a condition of human chimerism, shares similarities with some autoimmune diseases. The specific HLA genes of donor and host are known to be of central importance in graft-versus-host disease, and HLA class II genes are important in autoimmune disease. Considered together, these observations led to the hypothesis that microchimerism and HLA genes of host and non-host cells are involved in autoimmune diseases. Alternative sources of microchimerism include transfer from a twin or the mother during pregnancy, or from blood transfusion. Studies of systemic sclerosis, primary biliary cirrhosis, Sjögrens syndrome, pruritic eruption of pregnancy, myositis, and thyroid disease have both lent support and raised doubts about a potential role of microchimerism in autoimmune disease.