The X chromosome carries many genes that the Y chromosome does not. Having two copies of the X chromosome means that women are much less likely to suffer from X-linked recessive disorders, such as hereditary baldness and color blindness. However, new research suggests that being XX may also predispose women to autoimmune diseases, and may even make one sister in a set of identical twins more prone to disease than the other.

The X chromosome is the only chromosome that healthy people can possess in either one or two copies. Since men manage fine with just one X chromosome, how do women avoid getting conflicting messages with two different X chromosomes?

In a May 2003 article in New Scientist, David Bainbridge gives an informative overview of the workings of X chromosomes. In the 1960s, British geneticist Mary Lyon discovered that female mammals switch off one X chromosome in each cell, and bundle up the inactive chromosome in a structure called the Barr body. Which X chromosome is inactivated is random, and the process occurs early in embryonic development. Thus, adult females have patches of cells containing either an inactivated paternal or maternal X chromosome, and this phenomenon is called "mosaicism." Mosaicism explains why some female cats can be tortoiseshell, but tomcats can only be ginger or black. Although there are no tortoiseshell humans, the effects of mosaicism can be seen in women with anhidrotic ectodermal dysplasia. This X-linked condition reduces the number of sweat glands in the skin, and women with one faulty X chromosome have patches of sweating and non-sweating skin, each patch about one centimeter (0.4 inches) across.

Autoimmune diseases occur when some immune cells fail to recognize part of the body as "self," and attack that part as if it were a foreign threat. Many autoimmune diseases are more common in women than men, and sometimes the sex difference can vary by a factor of 50. Much research has focused on hormonal differences between women and men, but some scientists speculate that mosaicism may also increase women's risk.

As explained in the Bainbridge article, the thymus is responsible for training immature T cells to distinguish between "self" and "foreign." As they develop, immature T cells are educated by about 15 to 20 thymic cells, each presenting a fragment of "self" protein to test the T cell. Immature T cells that bind to "self" proteins are destroyed in the thymus, thus preventing the immune system from attacking the host's own body. This process of T cell education may be more error-prone in women, since an immature T cell may only encounter protein fragments from one X chromosome, and end up attacking the cells that use the other X chromosome. Furthermore, the educator cells may be biased in which X chromosome they use,