Bidirectional cell trafficking occurs routinely during pregnancy with the long-term persistence of fetal cells in the mother (fetal microchimerism) and maternal cells in her progeny (maternal microchimerism). Fetal DNA in maternal blood offers a noninvasive approach for prenatal diagnosis, including fetal Rhesus D genotyping, sex determination and diagnosis of single-gene disorders. Recently, we suggested that placental debris contributing to fetal DNA in maternal blood induces amelioration of rheumatoid arthritis during pregnancy and maternal tolerance of the fetus. Fetal and maternal microchimeric cells may have adverse health effects and are hypothesized to contribute to certain autoimmune diseases. Recent studies of microchimerism in prenatal diagnosis and the hypothesized link to the amelioration of rheumatoid arthritis during pregnancy and development of autoimmune diseases are described.