The immune system is a complex and highly developed system, yet its mission is simple: to seek and kill invaders. If a person is born with a severely defective immune system, death from infection by a virus, bacterium, fungus or parasite will occur. A key part of the immune system's role is to differentiate between invaders and the body's own cells - when it fails to make this distinction, a reaction against 'self' cells and molecules causes’ autoimmune disease.

Disorders of the immune system can be broken down into four main categories:

       1. Immunodeficiency disorders (primary or acquired)
       2. Autoimmune disorders (in which the body's own immune system attacks its own tissue as foreign matter)
       3. Allergic disorders (in which the immune system overreacts in response to an antigen)
       4. Cancers of the immune system

In severe combined immunodeficiency, lack of an enzyme means that toxic waste builds up inside immune system cells, killing them and thus devastating the immune system. A lack of immune system cells is also the basis for DiGeorge syndrome: improper development of the thymus gland means that T cell production is diminished.

Most other immune disorders result from either an excessive immune response or an 'autoimmune attack'. Asthma, familial Mediterranean fever and Crohn's disease (inflammatory bowel disease) all result from an over-reaction of the immune system, while autoimmune polyglandular syndrome and some facets of diabetes are due to the immune system attacking 'self' cells and molecules.