Recent studies have established that there is bi-directional cell traffic between mother and fetus during pregnancy. Suprisingly, fetal cells have been found to persist in the maternal circulation for years after pregnancy. Maternal cells can also persist into adult life in her progeny. When cells from one individual are present in the body of another the term chimerism is used and a low level of non-host cells is referred to as microchimerism. Chronic graft-versus-host disease often occurs after stem cell transplantation, is a known condition of chimerism, and resembles spontaneously occurring autoimmune diseases including systemic sclerosis, Sjögren's syndrome, primary biliary cirrhosis and sometimes myositis and systemic lupus. Of central importance to the development of chronic graft-versus-host disease is the HLA relationship of host and donor cells. Considering this constellation of observations together led to the hypothesis that microchimerism and HLA-relationships are involved in the pathogenesis of some autoimmune diseases. Although much additional work is needed, results of initial studies provide support to the concept that non-host cells could participate in the pathogenesis of some autoimmune diseases.