I thought this was an excellent description of how Candida overgrowth can lead to autoimmune disease. Taken from http://www.lightparty.com/Health/HealingRegeneration/html/Candidiasis.html
When undigested food particles penetrate the bowel wall and enter the bloodstream, the body views them as foreign invaders and makes antibodies (chemical bullets) against them. This can result in the development of food allergies or sensitivities, and ultimately autoimmune disease. There are some 80 known autoimmune diseases. The cause for all of them is officially “unknown.”
Among these autoimmune diseases are:
Chronic fatigue syndrome
The cause of these diseases may be unknown to mainstream medicine, but holistic practitioners are well aware of their connection to leaky gut syndrome. Since Candida is often the culprit behind the leak, we can view systemic candidiasis as an underlying condition, if not a cause, of allergies and other autoimmune disorders. Candida toxins are carried through the leaky gut (via the bloodstream) to the liver. From there, they proceed to other organs of the body — the brain, nervous system, joints, skin, etc. If the liver’s detoxification ability is impaired due to inadequate nutrition and toxic overload, these toxins will be stored and can initiate states of chronic disease.