Microchimerism is defined by the presence of circulating cells, bi-directionally transferred from one genetically distinct individual to another. The acquisition and persistence of fetal cell microchimerism, small numbers of genetically disparate cells from the fetus in the mother, is now a well-recognized consequence of normal pregnancy. Some of the autoimmune diseases that show a predilection for women in their child-bearing years and beyond are linked to fetal microchimerism from previous pregnancies. Microchimerism has been investigated in different autoimmune disorders, such as systemic sclerosis, systemic lupus erythematosus, autoimmune thyroid diseases, and primary biliary cirrhosis. Recent data have demonstrated the promising role of microchimeric cells in the maternal response to tissue injuries by differentiating into many lineages. Therefore, further understanding of fetal-maternal microchimerism may help in anticipating its implications in disease as well as in more general women's health issues.