How Does Your Immune System Work?

Understanding how your immune system works can help you learn the best ways to keep it functioning optimally and enhance your health. Your immune system is an astonishing, fascinating, and complex network of organs, tissues, and cells that exist to protect your body from foreign invaders and tumors. You might think of it as a Superhero or a branch of the military. It forms natural barriers to keep invaders out of the body and launches direct attacks to get rid of any that manage to penetrate the barriers and infect the body.

Immune cells travel around the body looking for bad guys (bacteria, viruses, yeast or fungi, toxins, cancer cells, or anything foreign), that will harm you; when they are found, they are destroyed and disposed of quite efficiently.

The ability to distinguish between “self” and “non-self” is crucial so that the immune system does not attack body tissue, so remarkably, other cells in the body (self) are distinguished or “marked” by a particular type of protein. This allows immune cells to coexist peacefully with other body cells and recognize the invaders.

A non-self substance that has the ability to incite an immune response is called an antigen. The immune system will launch an attack anytime it encounters a non-self substance (antigen). An antigen may consist of an entire microbe like a virus, bacteria, yeast, or parasite, or it may consist only of a fragment of that microbe like a molecule. Cells and tissues from another human being are also “marked” as non-self, unless it is your identical twin, and will be perceived as antigens. Thus, the reason that organs may be rejected in an organ transplant.


Cytokines are chemicals that are used in cell-to-cell communication within the immune system, which may be referred to as interleukins, interferons, and growth factors. For example, one type of white blood cell will use cytokines to notify another type of white blood cell about an invader and instruct them to strike. They can turn on or off particular types of immune cells and stimulate the production of T cells.

There are many different types of cytokines and some are pro-inflammatory and others are anti-inflammatory. The proinflammatory produce inflammation when fighting off an invader and the anti-inflammatory being activated to reduce inflammation once the invader is eradicated.

Organs in the Immune System

Organs in the immune system are referred to as lymphoid organs and are located in various spots throughout the body. These organs house and deploy the immune cells and are attached to one another and other organs in the body via the lymphatic vessels.

  • Tonsils (back of throat)
  • Adenoids (between your nose and the back of throat)
  • Thymus (in center of chest)
  • Spleen (left side of the abdomen)
  • Bone marrow (soft center of all bones)
  • Lymph nodes (distributed widely throughout the body like armpits, neck, breasts etc.)
  • Lymphatic vessels (distributed widely throughout the body)
  • Appendix (lower right of abdomen)
  • Peyer’s patches (organized lymphoid nodules in the lower part of the small intestine called the ileum

Immune System Cells

When a foreign invader is found, then the immune system may use a variety of different weapons in its arsenal (known as white blood cells or antibodies) to get rid of it, depending on the situation. The big players on the team consist of lymphocytes, neutrophils, eosinophils, macrophages, basophils, natural killer cells and immunoglobulins. They can travel through blood vessels or the lymphatic vessels.

Some cells can display a wide variety of skills and destroy many different kinds of invaders, while others are highly specialized in one particular area and go after only a particular type of pathogen. They rally together as a team and use an elaborate and complex communication system to devour, puncture, blow up, inject, or spray the invaders with chemicals.

For example, one cell may flag an invader as an antigen and call in another type of cell to gobble it up or spray it with chemical, then another cell will hang around to make sure it doesn’t come back.

Like all cells, immune cells develop from stem cells in the bone marrow. They are instructed by cytokines and other chemical messengers on which type of cell they should grow into.

Blood vessels and lymphatic vessels exchange cells and fluid, which allows the lymphatic system to cover the tissues of the body with a clear fluid called lymph; keeping an eye on the rest of the body for foreign intruders.

Lymph nodes are dispersed throughout the lymphatic vessels and congregate in areas like the armpits, groin, neck, and abdomen. They house clusters of immune cells within specialized compartments where they can confront antigens.

The spleen also contains specialized compartments where immune cells congregate and encounter antigens. It also filters the blood.


Some lymphocytes mature within the bone marrow and are referred to as “B” cells, while others will be sent to the thymus to mature and are referred to as “T” cells. Both will identify and destroy invaders but in a slightly different way.

The B cells produce antibodies against the invader (called humoral immunity or antibody production) but they are not capable of penetrating a cell. Each B cell is hard wired to produce only one particular type of antibody and is activated whenever it encounters the antigen it is designed for, at which time it produces plasma cells that then produce the antibodies.

T cells don’t identify free-floating antigens, they may instruct and regulate the immune response or attack an infected or cancerous directly. They destroy the organism by killing the body cell that is infected with a microbe or cancer cells; or releasing a chemical called lymphokines that will incite an immune response to attack something like a virus or cancer cell, (called cell-mediated immunity).

Some lymphocytes travel around and patrol the body through lymphatic vessels and the bloodstream, while others will be stored in the lymphoid organs. Most lymphocytes are T cells.

There are several types of T cells and each one has a unique job, which include:

  • Helper T Cells – as the name implies, these cells help support the rest of the immune system. They will use cytokines to call in macrophages, activate B cells that produce antibodies and fuel production of cytotoxic T cells and suppressor T cells. Helper T cells are the cell that is affected in HIV.
  • Cytotoxic T Cells – these cells excrete chemicals that fracture and destroy the foreign invaders like cancer and viruses or other cells that have been harmed in some way.
  • Natural killer cells are part of the innate immune system and a type of cytotoxic T cell that bind with cancer cells, or other cells infected with microbes like viruses, bacteria or fungus, and then inject them with a deadly toxin to kill them. You can think of them as the Special Ops branch of your immune system; they move in very quickly and stealth like and do not need prior information about the antigen to make a strike. They may slay anything that is non-self on contact.
  • Additionally, natural killer cells, assist in regulating the immune response by releasing cytokines that instruct other parts of the immune system to kill an invader. If natural killer cells are not functioning properly it may result in some types of autoimmune disease like type 1 diabetes, asthma and cancer growth.
  • Memory T Cells – stick around after an attack in case the invader returns to the scene. These cells are quite “intelligent”, they will keep a “record” of all the invaders that have affected your body, and remember them, so they can deal with them more efficiently if they try to invade the body in the future.
  • Suppressor T Cells – keep the immune system from getting out of control and harming healthy cells and tell it when to back off.

Immunoglobulins (Antibodies)

Antibodies, also known as immunoglobulins, are molecules shaped like a Y that ambush and bind to antigens, leading to them being neutralized or broken open and destroyed by other parts of the immune system. They may mark a particular pathogen like yeast or bacteria so that it can be found by another immune cell to eliminate, or it may take some steps itself to neutralize it. There is a specific antibody for each individual antigen. For example, one antibody will take care of the flu virus, while another antibody will target a bacteria; they are not interchangeable.

So essentially, the antibody puts a little a flag on the antigen that tells the white blood cells, “hey guys here’s one, come and get him.”

Antibodies also activate the complement system, which is part of the innate immune system consisting of about 25 proteins that support antibodies and assist other parts of the immune system in eliminating an invader. It can help motivate neutrophils and macrophages, as well as neutralize or break apart invading organisms. They also help get rid of antigens that are coated with antibodies and are one of the substances that contribute to symptoms like warmth, swelling, pain, redness, and loss of function in an inflammatory response.

The five primary types of antibodies or immunoglobulins include IgA, IgG, IgM, IgE, and IgD:

IgA is present and guards all mucosal surfaces throughout the body like the nose, ears, eyes, gastrointestinal and respiratory tract, and vagina, as well as fluids like saliva, blood and tears. Approximately ten to fifteen percent of the antibodies in the body are IgA.

IgG puts a coat on microbes to increase the speed by which other cells in the immune system can gather them up and can be found in all body fluids. They are vital for eliminating bacteria and viruses. IgG antibodies are the smallest and most common antibody in the body, making up about seventy-five to eighty percent. They are the only antibody that can travel across the placenta of a pregnant woman to her unborn child to provide it with protection.

IgM antibodies are potent against bacteria and can be found in the blood and lymph fluid. About five to ten percent of all antibodies in the body are IgM and they are the largest antibody. IgM antibodies are the first antibody to be made when a response is launched and they assist other immune cells in destroying foreign invaders.

IgE is in charge of safeguarding against parasites and is also what prompts the reaction to, and allergy symptoms of, things like animal dander, pollen, mold, food, medications, and poisons. They are found in the skin, lungs, and mucous membranes.

IgD remains connected to B cells where it plays a primary role in launching B cell responses promptly. They are found in tissue that lines the stomach and chest and are not completely understood.

If your body does not produce enough antibodies, you may be more vulnerable to infection and disease. Some people are born with a reduced capacity to produce antibodies, and production may also be stunted in response to some diseases like cancer.

Your doctor may run an immunoglobulins test that will measure the levels of antibodies in your body to help determine whether your immune system is functioning as it should or identify specific conditions or issues. They may use an immunoglobulins test to identify autoimmune diseases, allergies, cancer, infections, the efficacy of treatment against something like h pylori, monitor response to immunizations or determine whether an infection is new or old.

For example, the presence of IgM antibodies for mononucleosis with or without IgB antibodies indicates a new infection, while the presence of IgG without IgM indicates a past infection. Since all antibodies are unique for each organism (an antibody for the flu is different than an antibody for herpes) this can tell your physician what you are dealing with specifically. You could be tested for antibodies against Candida, the Lyme spirochete, herpes, h pylori, a variety of different foods, or many other things.

IgE levels will be high in people with allergies or a parasite infection and some types of cancer and autoimmune disorders and rarely multiple myeloma (cancer that begins in the plasma cells in bone marrow).

IgG may be high in people fighting off bacteria. They may indicate a chronic, long-term infection is present, or multiple myeloma, long-term hepatitis, or MS.

IgM may be high in early viral hepatitis, mononucleosis, kidney damage, parasite infections, and rheumatoid arthritis. Since IgM is the first antibody at the scene of the crime, the presence of IgM may indicate a new infection rather than an old one.

High levels of IgA may indicate multiple myeloma, an autoimmune disorder like lupus or rheumatoid as well as cirrhosis and long-term hepatitis.

IgD may be high in multiple myeloma as well, but less common than IgA or IgG-mediated.

If IgA levels are low, it may allow microbes to proliferate in the gut and it may also indicate leukemia, kidney disease, or a rare disease that is inherited that affects muscle coordination called ataxia-telangiectasia. Some people are born without any or very low levels of IgA antibodies.

Low levels of IgG may also be the result of some types of leukemia and kidney damage as well as macroglobulinemia (cancer of the B lymphocyte cells). Some people may also be born with a low level of IgG antibodies and are more vulnerable to infections.

Low levels of IgM may occur in some types of leukemia or other immune diseases that are inherited and multiple myeloma.

While IgE may be low in ataxia-telangiectasia as well.

However, do note that these results should always be interpreted by a doctor, as there are many other factors that must be taken into consideration.

Phagocytes & Other

Phagocytes, which include neutrophils, eosinophils, and monocytes (macrophages), are another type of white blood cell that actually gobble up, devour, engulf or eat pathogens. They also absorb dead cells in our body and help wounds to heal. Neutrophils and macrophages take care of bacteria and fungi, eosinophils primarily target parasites. Basophils are connected with allergy-related antigens.

Macrophages are monocytes that are in the tissue, while they are in the bloodstream they are called monocytes. A macrophage may also present an antigen to other lymphocytes and produce a chemical signal called monokines that are used in the immune response.

Neutrophils contain chemicals that break down the invaders they consume and eosinophils and basophils will spray chemicals onto harmful microbes or cells.

Granulocytes are a type of immune cell that contain granules that are filled with powerful chemicals that kill microorganisms. One of these chemicals is known as histamine, which contributes to allergy and inflammation.

Mast cells, which are not really blood cells, but function similar to basophils are found in parts of the body like the nose, lungs, tongue, skin and also play a significant role in allergy symptoms.

Platelets which are used for blood clotting and repair of wounds, also activate some immune activity, and dendritic cells which reside in lymphoid organs can help stimulate T cells and can present antigens to the T cells.

Your doctor may order a white blood count test to see if you are fighting an infection. An increase in any of these types of white blood cells indicates there is an infection. Some conditions may result in a decrease of production like cancer or bone marrow disorders.

Layers of the Immune System

Microbes can enter through the mouth, nose, lungs, gastrointestinal tract, eyes, genitals, and skin. However, each of these organs has a variety of protective mechanisms in place that the microbe must penetrate first. For example, the skin is like a suit of armor and can only be penetrated if there is a cut or an abrasion. The stomach secretes a variety of enzymes that will destroy microbes, the nose will produce mucous, and the lungs will cough.

If the microbe manages to get past this first line of barriers, then it must penetrate the second line of defense which consists of a thick layer of epithelial cells covered with mucus that lines all the passageways (respiratory, gastrointestinal, and urogenital), forming a protective barrier. Not only that, the mucus lining also secretes IgA antibodies that will capture approaching invaders. If the microbe manages to get past all these barriers, then B cells, T cells, and macrophages lie in hiding just below the epithelial cells.

Then they will be confronted by the innate immune system and attacked by phagocytes, natural killer cells, and the complement system. The innate immune system is always present, but its response is immediate, short-lived, generic and non-specific.

Next they will face the adaptive immune system where T cells and antibodies have ammunition that is designed specifically for each individual type of microbe. The adaptive immune system is called on when invaders overcome the innate immune system. It provides highly specialized and long-lasting immunity that is acquired from encountering pathogens and learning how to handle them better next time. There are two types of responses within the adaptive immune system, called humoral immunity (moderated by antibodies that are produced by B cells) and cell-mediated immunity (moderated by T lymphocytes).

Each microbe is handled in a unique way. For example, bacteria reside in between cells, where antibodies bind with them and then call on the complement system and phagocytes to destroy them.

Viruses, as well as a few parasites or bacteria, can only survive by actually entering body cells, so specially designed molecules are used to bring pieces of the microbe to the surface, which alerts cytotoxic T cells to come in and exterminate the infected cell. Alternatively, antibodies may bind with and destroy the virus before it has a chance to get in the cell.

A parasite may survive either within or outside the cell. An intracellular parasite will be confronted by T cells, while an extracellular parasite demands a more comprehensive approach including antibodies that draw in eosinophils, basophils, and other specialized granule-containing cells to hustle in and disperse their arsenal of toxic chemicals.

Natural and Acquired Immunity

There is natural immunity and acquired immunity. Natural immunity is natural barriers that you are born with like your skin, epithelial cells or antibodies passed from mother to child. Acquired immunity is the result of being exposed to a particular pathogen or toxin and memory cells learning and then remembering how to kill a particular invader if it comes back in the future.

Acquired immunity is utilized in vaccinations. If you give the body a diluted amount of a particular antigen, the body will learn how to get rid of it, so if the same antigen presents itself in full force later, the body will already know what to do and keeps you from getting sick. Unfortunately, vaccines contain a variety of toxins that are actually harmful to the body, so they do more harm than good.

The Immune System in Action

Imagine if you will that you have you cut your finger. These amazing cells immediately gather around the source, send out an alarm to other cells, share information with one another, send out signals to other cells, call other cells in to help them, generate powerful chemicals, kill the invaders, help the wound heal, leave sentries behind to watch out for reinfection, and yet still patrol the rest of the body for any other potential trouble spots. All of this is done automatically for you without any effort on your part. This is truly nothing short of astounding and should leave you with a sense of awe.

Immune System Disorders

Sometimes things can go awry in the immune system; it may become suppressed or overactive, it may confuse self for non-self or hit the wrong target. When this occurs, then a barrage of many different types of disorders may develop, like allergies, autoimmunity, arthritis, and cancer and one may be left vulnerable to invasion by a wide variety of microorganisms.

For example, if the immune system confuses self for non-self, it may produce antibodies against your own tissue and/or launch an attack against the body’s own tissues or cells, which results in an autoimmune disorder like lupus, arthritis, or thyroiditis. If the immune system becomes hypervigilant and goes after substances that are not really harmful to us like pollen, then allergies develop. If immune cells become impaired for some reason or are not available in sufficient numbers, then a microbe may enter the body and get the upper hand and one develops an infection.

Furthermore, if the body becomes infected with a stubborn and hard to eliminate microbe, the immune system will be in constant battle with the organism. This results in a high level of oxidative stress and inflammation from all the chemicals it is spewing out and the war between them. The oxidative stress and inflammation themselves can then lead to a wide variety of other health problems and premature aging.

Some microbes like bacteria, Candida yeast, and parasites have the ability to form a structure called a biofilm that allows them to hide out from the immune system and avoid annihilation. When that is the case, the biofilm must be destroyed before the immune system can go to work.

A poor diet, environmental toxinschronic stresslack of sleep, impaired gut flora can all be underlying factors that impair immune function and lead to these disorders. Now that you have the answer to how does your immune system work, you can help keep it functioning more optimally, by eating a healthy primal dietliving environmentally friendlymanaging your stress, getting adequate sleep and supporting the healthy flora in your gut.

How Does Your Immune System Work References

  1. The Immune System
  2. National Institute of Allergy and Infectious Diseases
  3. Functions of Natural Killer Cells
  4. How Neutrophils Kill Microbes
  5. Immunoglobulins

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