The Underlying Cause of Chronic Disease

The New Paradigm in Heath Maintenance and Disease Progression
Part II: What Causes Inflammation?

Today we will discuss what causes inflammation from a functional medicine perspective. In Part I we reviewed some basic concepts about inflammation and what it is. When in balance, inflammation is a good thing that helps to heal us and maintain our systems integrity. When out of balance; disease, poor healing, poor health and even cancer can result. The natural questions that now come to my mind are: What causes inflammation? and How can I prevent it?  The last part of this will be dealt with in Part III, where we discuss functional medicine treatments for inflammation.

Part Two:

What Causes Inflammation?

A variety of things can cause inflammation ranging from infections to injuries. We will discuss five major causes of inflammation and consequently immune system dysregulation. This list is not exhaustive but will provide you a basic understanding of inflammation causes.

The five major causes of inflammation are:

  1. Trauma
  2. Infections
  3. Deficiencies
  4. Toxins
  5. Stress


 Most of us are familiar with physical trauma from life experience. You twist an ankle or fall and hit your thigh and get the classic signs of inflammation we have recognized since Dr. Virchow’s time in the early 1800’s. These signs of inflammation that comes from trauma are redness, heat, fever, swelling and loss of function. Trauma best characterizes all of these signs yet any cause of inflammation can cause any one or all of the above.

After the initial trauma, the contents of the damaged cells are released as well as chemical mediators (the cytokines from Part I) that recruit your immune system to act. Cell eating cells (i.e.- macrophages) first come in to recycle the dead and damaged tissue. New progenitor cells (cells that makes new similar cells) follow the cell signals and come to the local area and lay down new structures for the healing tissues to attach to. Finally, balance is again achieved in the local tissues and the system goes back to business as usual.

However, this can become dysregulated if the system is overwhelmed or dysregulated. The local inflammation and healing process can become generalized and involve the whole body. Organ systems can become overloaded and organ failure can occur. This is what happens after a major physical trauma like a fall or car accident. Again, this process also can be caused by other things besides trauma; like infections, toxins, and deficiencies.


Infection in the body is another familiar cause of inflammation. Most of us have had strep throat. You ache all over, get red large hot looking tonsils, and are laid up in bed for a few days. These are similar signs of inflammation as in trauma but in this case, it’s limited to an infected body part. Again, your immune system comes to the rescue, walls off the infection, attacks it, kills the infected cells, repairs the damaged tissue and in a week, you are as good as new.

This system can also become derailed. If, for example, you are colonized with strep and genetically vulnerable, your body can make antibodies that attach to your heart (e.g. Rheumatic Heart Disease), your kidneys (e.g. glomerulonephritis) or even in young children your brain (e.g. PANS or PANDAS). Certain viruses that are suppressed can become reactivated and result in a limited disease (like shingles from the chicken pox virus) or even certain cancers (like Burkitt’s Lymphoma from the EBV virus). There are too many examples to list here (e.g. Chronic Lyme’s Disease, Chronic Mono) but you get the idea. Both acute and chronic infections can cause inflammation.

Hopefully you are starting to see a pattern. Balance in our bodies’ systems is crucial for health. Anything that can cause imbalance, can affect our health resulting in chronic inflammation.


Deficiencies is the first of several causes of inflammation that are unfamiliar to most of my patients. There is data associating chronic selenium deficiencies to viral infections and even certain types of heart disease. Vitamin D deficiency in the winter months is associated with an uptick in influenza and other winter infections. Vitamin C deficiency is associated with poor dental health as well as poor wound and injury healing. Vitamin B12 deficiency affects nerve function and repair as well as folic acid deficiency affecting the repair of your gut lining. Though vitamin and mineral deficiencies are not specific to inflammation they do affect our bodies natural healing processes and result in low grade chronic inflammation due to immune system dysregulation.

A common misconception is that nutritional deficiencies are rare in the US This can’t be farther from the truth. According to the textbook Nutritional Medicine by Alan Gaby M.D., 80% of Americans are deficient in magnesium, 40–60% are deficient in any one of the B vitamins and 30% of American are deficient in Vitamin D. Added together, the average person has multiple nutrient deficiencies. These affect immune system response rates, degree of response, order of response (over or under response) and if the response turns off or remains chronically on.


This is another overlooked cause of inflammation, toxic. Often, my patients do not understand or cannot define a toxin or toxicant. A toxin is a substance produced by another living organism or a natural substance that can cause damage to the human body. An example would be poisonous mushrooms. A toxicant is a man-made substance that can cause damage and/or disease to your body. An example would be a pesticide. For simplicity most people use the term toxin for both, which we will do here as well.

Toxins can be acutely inflammatory, as in a high dose exposure to a chemical, or they can cause low grade inflammation by chronic low grade exposure. This is what I want to focus on here. This process is commonly referred to as Toxin Induced Loss of Tolerance (TILT). The basic concept is that a low-grade exposure to a chemical or heavy metal will bind to proteins in your body and create a structure your body doesn’t recognize. This activates your immune system to come and clear out the substance, but because the exposure is ongoing, the low-level inflammation does not resolve. Eventually your immune system can become so disorganized that it creates antibodies to the altered proteins that will also react against healthy cells. This is called Molecular Mimicry and is emerging as a cause of autoimmune disease.

The issue with toxin exposure is that it is not a simple one-to-one correlation; it is a complex interaction of differing toxins. The average female puts over 150 chemicals on her body each morning before going to work. There are over 80,000 chemicals that have been produced or are in production in the US and many of these find their way into the environment. To date, all safety studies are on single chemicals and fail to take into account their interactions within the human body.


Stress is one of the most pervasive yet unknown causes of inflammation in our country today. The field of stress induced inflammation is call Psychoneuroendoimmunology, or PNEI for short. The basic concept is that stress in your mind releases signaling molecules that travel via your nervous system to all the organs attached to your nervous system. The effect is especially potent on your hormone system (endocrine) and immune system. Over time, the chronic stress that initially cause a heightened sense of hormone and immune response results in the down regulation of these systems and eventually—if left unchecked—their dysregulation.What does this look like in real life? Imagine that someone or something scares you. Your innate nervous system response is to activate your adrenal glands to release adrenalin to speed up your heart, muscles, and brain for action. At the same time, your pancreases is stimulated to release a hormone called glucagon to elevate your sugar levels to also prepare you for rapid action. The Vagus nerve to your gut slows down digestion and diverts blood flow to your muscle from your Gi tract organs. All this happens instantly—pretty awesome! If, however, the stressor does not resolve over time, your sleep can become disrupted, you can develop insulin resistance (a precursor to diabetes), you can start to get digestive tract issues and food intolerances and markers of inflammation and immune system dysregulation will elevate in your blood.

The problem with the above is that your body can’t discern the difference between a life-threatening stressor and a benign one. So your body’s response to the daily stressors of being late to work, stuck in traffic, or worrying over events in your news feeds is the same as if you were going through a life threatening stressor like a famine or major migration caused by war. These chronic stressors can eventually affect your hormone levels, immune system dysfunction and even memory. But at the cellular level the final common denominator for all of these is inflammation.

Hopefully after reading about the causes of inflammation you aren’t stressed or left feeling there is nothing you can do to prevent inflammation. In Part III, I will discuss treatment options for inflammation and what you can do to combat its ongoing effects.

Icon Credit
Trauma Icon created by Artem Kovyazin
Infection Icon created by Sergey Demushkin
Low Battery Icon created by Jonathan Li
Stress Icon created by Thomas Helbig
From TheNounProject