Tolerance is the lack of an immune response to self. MHC molecules (gene products from MHC genes) control the body's ability to recognize self and non-self. When T cells mature in the thymus, they are checked for their reactivity against self. Normally all T cells which react against self are destroyed. Inappropriate T cells produced in the thymus, about 95% of the total, die and never enter the circulatory system. T cells in the circulatory system must receive signals from normal cellular tissue to survive. When these control systems fail, the immune system can react against our own molecules.

Autoimmunity is an immune response against self (auto=self).Autoimmune diseases occur when the body attacks its own tissues. Rheumatoid arthritis, myasthenia gravis and lupus (systemic lupus erythematosus) are examples of autoimmune diseases.