Immune system diseases can be divided into two basic categories. There are dysfunctions or diseases of the immune system in which the body's ability to fight disease is impaired and dysfunctions or diseases of the immune system in which the immune system overreacts to stimuli, causing damage to the other organs or systems of the body.

There are numerous rare congenital or inherited diseases of the immune system and these are frequently referred to as primary immune deficiency diseases. These immune system diseases affect an estimated 50,000 people in the United States. A healthy immune system recognizes "invaders" such as viruses, bacteria or anything that is not a normal part of the body and destroys these invaders. In cases of severe immune system diseases, the body may have little, if any, normal immune responses. These diseases of the immune system result in frequent recurring infections. Nezelof's Syndrome, Granulomatous Disease, T-Lymphocyte Deficiency, Chronic Dysphagocytosis, Impotent Neutrophil Syndrome and Congenital Dysphagocytosis are all examples of immune system diseases in which there is a weakened or absent response to everyday bacteria, viruses, fungi, etc.

Acquired Immune Deficiency Syndrome (AIDS) is one of the immune system diseases that is not inherited or congenital. It is caused by an infection with the human immunodeficiency virus or HIV. HIV invades and inactivates certain cells of the immune system, known as helper T-cells. Helper T-cells are white blood cells that normally stimulate the production of antibodies and killer T-cells, which destroy viruses, bacteria and other invaders such as cancer cells. As opposed to the other rare diseases of the immune system, which may be caused by a missing or inactive spleen or thymus or some other congenital or inherited defect leading to a lack or absence of any white blood cells, a person who suffers from AIDS had a previously healthy immune system. According to the Center for Disease Control and Prevention (CDC), an estimated 944,305 people in the United States have been diagnosed with AIDS.

There are many conditions which are believed to be caused by dysfunction of the immune system and these are sometimes referred to as diseases of the immune system or are grouped together with diseases of the immune system for purposes of discussion. Rheumatoid arthritis, for example is believed to be caused by an "overactive" immune system. Diseases such as lupus, juvenile onset diabetes, multiple sclerosis, and psoriasis are all believed to be related to an overactive immune system. Diseases like these are characterized by immune system attacks on healthy normal cells for unknown reasons. Even allergies are believed to be related to dysfunction of the immune system, since the immune system overreacts to allergens.

Much about how the healthy immune system works is unknown. Most of what we know about a healthy immune system has been learned by studying diseases of the immune system. Much of what we know about health supplements that help support and maintain a healthy immune system arises from the study of immune system diseases and efforts to treat them.