Your immune system can mistake your own tissues for invaders and attack them. Hashimoto's thyroiditis, where the body attacks the thyroid, is one common example. Once the system identifies self as foreign, it produces antibodies and inflammatory molecules against it.
If we make it as simple as possible, autoimmunity is exactly what the name says. It is some part of your immune system has gotten off track and it's doing the right thing in the wrong place. So instead of attacking an invader or helping you modulate your immune function for infection or healing, it's decided a part of you or parts of you are the enemy. But the real problem is that once your immune system gets the idea chemically that a piece of you or pieces of you are an outsider or the enemy, they will start to make antibodies and other inflammatory chemistry against that part of you. One of the most common is Hashimoto's thyroiditis, which large numbers of people have.
