Multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis share common features in typical cases such as: adult onset, central nervous system problems, female predominance, episodes triggered by a variety of stresses, and an autoimmune reaction. At times, the different disorders are found in the same patient or close relatives. These disorders are quite complex but they may share a common mechanism that results in different, tissue-specific consequences based on the cell types in which the mechanism occurs. Here, it is hypothesized that DNA damage can lead to loss of epigenetic control, particularly when the damaged chromatin is distributed unevenly to daughter cells. Expression of genes and pseudogenes that have lost their epigenetic restraints can lead to autoimmune disorders. Loss of control of genes on the X chromosome and loss of control of polyamine expression are discussed as examples of this mechanism.