The immune system can differentiate between molecules that are part of the body, i.e., self-molecules, and molecules that are not a part of the body, i.e., non-self molecules. The organs of the immune system include: Table of Immune System Organs

Primary Lymphoid Organs

Bone Marrow
Thymus Gland

Secondary Lymphoid Organs or Tissue

Lymph Nodes
Spleen
Lymphoid Tissue in skin and mucosal areas such as the gut and respiratory system

Thus, it is the basic function of the immune system to eliminate these non-self molecules. These non-self molecules might be in the form of bacteria, viruses, protozoa, fungi, cells infected with these parasites, cancer cells, or other molecules in the environment that enter the body and are"perceived" by the cells of the immune system as foreign substances. Thus, the cells of the immune system are activated by presence of non-self molecules.
Inflammation is a basic immune response to the introduction of foreign antigen into the body. It involves a complex series of reactions, initiated through damage of endothelial cells, that:

increases circulation to the area of injury through the release of vasodilators by cells such as mast cells or basophils;
increases the concentration of plasma proteins involved in the Acute Phase Response. One such protein, C-reactive protein, can function as a non-specific opsonin;
results in tissue swelling via leakage of plasma into the area of injury;
activates the classical complement system via the proteolytic enzyme plasmin resulting in the lysis of the parasite or its' opsonization and removal via phagocytosis;
results in the release of cytokines by endothelial cells and platelets that attract immune system cells (lymphocytes, polymorphonuclear cells, and monocytes) to the area of injury.

The inflammatory response, while eliminating the foreign antigen or parasite, can, as well, result in local tissue damage. In cases of hypersensitivity (asthma/allergy), the response may result in anaphylaxis; if directed at a self antigen, in an autoimmune disease.
The cells of the immune system inculde: Table of blood cell types

Lymphocytes

T-helper cells:
secrete hormones called cytokines that activate other cells of the immune system.
Cytolytic T- cells or CTL:
eliminate cancer cells or cells that are infected with a parasite. Foreign antigen is processed and then presented on the surface of the infected cell. This non-self protein is recognized as such by the CTL and the infected cell is lysed.
B-lymphocytes:
secrete antibodies or immunoglobins. These are protein molecules that are specific for a particular molecule (antigen). Antigen can be individual molecules, or molecules that are part of a virus, bacterium or some other parasite. Antibodies bind to the antigen (pathogen) resulting in their neutralization through two possible mechanisms; complement mediated lysis and antibody dependent cellular cytotoxicity (ADCC), facilitating antigen (pathogen) removal from the body by natural killer cells or phagocytic cells.
Plasma proteins, secreted by the liver and collectively called The Complement System, are activated by the binding of antibody to antigen. They attach to the antibody and can lyse the virus or cell.
Natural killer cells (NK Cells):
eliminate cancer cells or cells infected with a parasite by lysing these cells. NK cells have receptors that recognize self MHC class 1 molecules. It is the failure of expression of MHC class 1 molecules on a cell that results in cellular lysis.

Macrophages:
phagocytic cells that can eliminate a parasite or a cell infected with a parasite. They produce nitric oxide, lytic enzymes and other molecules such as hydrogen peroxide that aid in this process. Macrophages are also antigen presenting cells. They process a foreign molecule to a form that can activate T-helper cells.

Dendritic cells:
antigen presenting cells.

Neutrophils, Eosinophils , Basophils, and Mast cells:
neutrophils and eosinophils are phagocytic cells that can eliminate a parasite or cell infected with a parasite; basophils and mast cells secrete molecules that assist in the immune response.

The cells of the immune develop from pluripotent cells called stem cells. This development occurs in the bone marrow. It is completed in the bone marrow with the exception of T-lymphocytes. Immature T-cells migrate from the bone marrow to the Thymus Gland where the complete their maturation. In the thymus, T-cells undergo a process of positive and negative selection that eliminates auto-reactive cells.
Various proteins are expressed on the cell membrane of the cells of the immune system. Some of these membrane proteins can be cell type specific or shared with other cells. If cell specific, these molecules can by used, in combination with other techniques, as "markers" for the identification and isolation of a particular cell. For example, T-helper lymphocytes express a molecule called CD4; Cytotoxic T-lymphocytes express the CD8 molecule. There are many other molecules expressed on these as well as other cell types that can be of diagnostic and therapeutic benefit.

This is but a very brief and incomplete outline of the immune system and immune system function. Additional information at: IMMUNE SYSTEM , and, an excellent reference text by Abbas, Lichtman, and Pober published by W. B. Saunders Company.

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