A normal immune system reacts when the body identifies a foreign protein such as proteins on the outside of bacteria. This foreign material which invokes the immune response is called an antigen. The body can react to the antigen by producing protein molecules (antibodies) which bind to the antigen. In addition to antibodies, various cells are activated in an immune response and either directly kill the foreign agent such as a bacteria, or release chemicals which help in the destruction.

In autoimmunity, the immune system has lost the ability to distinguish between foreign antigens and its own tissues. The prefix 'auto' means 'self,' so autoimmunity describes an immune system that destroys portions of its own body. It views its own normal tissues as foreign antigens and attempts to destroy them. An example is pemphigus foliaceus, a skin disease in cats which often affects the head and feet. In this instance, the cat's immune system erroneously perceives its own cells in the skin as abnormal. It destroys them causing the skin lesion. Chronic gingivitis and stomatitis (a serious gum disease) in cats appears to have autoimmune components to the disease process as well.

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