The Functional Medicine Matrix


In the Functional Medicine model, the body’s function is viewed in light of seven fundamental systems. The Functional Medicine Matrix is a useful tool that assists Functional Medicine practioners to organize and prioritizing a patient’s health issues through a variety of factors such as family history.

What Is The Functional Medicine Matrix?

The Functional Medicine Matrix can be thought of as a web decoder,  the matrix takes into account how the environment interacts with your genes and can result in health or disease. Helping to group and organize seemingly unlinked factors to paint a comprehensive picture of the patient and their life which can then be used to discuss chronic disease with said patient.

The factors that make up the matrix are as follows:


This is how your body breaks down the foods you eat and the water you drink and then converts the break down products into energy and nutrition for your body. This process starts in the mouth and ends at the cell level where the final products are utilized. The nervous system interacts with the GI tract in controlling transit and digestion. The hormone system interacts with the GI tract in producing digestive hormones. Your blood and hematologic system carry the nutrition to all the parts of your body and finally your immune system evaluates the potential danger of all that enters your body and 99.9% of the time determines it is safe, if this interaction is overstimulated chronic inflammation can occur.

Biotransformation & Elimination

These processes account for the way your body interacts with your nutritional inputs and then converts the waste products of metabolism into non-threatening inert compounds that can then be excreted from your body. If these don’t perform correctly toxic compounds and metabolites can slowly build up in your system over time. Your biochemical systems have to convert solid food, liquid drink, and gaseous air into the most basic elements that can nourish each cell in your body. Your body has multiple redundant biochemical systems to facilitate this. However in some individuals—due to nutritional deficiencies, toxin or toxicant exposures, genetic mutations, chronic stressors or chronic inflammation the cellular—systems won’t function property resulting in a slow breakdown in function.

Defense & Repair

This system is generally thought of as your immune system and its interaction with your body’s general tissue repair systems. Your immune system has the task of identifying enemies from within and without and then facilitating cellular repair when the inflammatory assault on the invader is finished. Every cell in your body has an immune system tag that tells it not to destroy that particular cell. Then, when a cell dies the immune system recognizes the changes in the tags of the dead or dying cells and goes in and cleans them up. Your cells are also preprogrammed with an ‘auto destruct’ program call apoptosis. If the cell becomes diseased or sick it will die and again your immune system will clean it up, and then assist in tissue repair. If this system becomes dysregulated, chronic inflammation becomes rampant; this can result in autoimmune diseases or immune system and repair dysfunction and chronic inflammation. These symptoms are diffuse and range from chronic fatigue, to aches/pains, joint inflammation and in some patients chronic relapsing and remitting fevers and illness.

Structural Integrity

The structural integrity category is a little more complicated and diffuse but can best be thought of as cellular integrity. Things need to stick together in order to function. If the bricks in your house fall out of place one by one, eventually the whole house collapses. Cellular integrity includes that of your arteries and veins as well as that of your tissues. However, tissue breakdown starts at the cellular and arteriolar level. So, we typically view cardiovascular disease as its own specialty and in Functional Medicine it is given a whole study module yet the same processes that cause heart attacks and strokes also decrease kidney function, brain perfusion and blood flow to the entire body. So the break down in vascular integrity that starts in the teen age years doesn’t result in heart disease for decades yet the same process is ongoing in the entire body, not just the heart. It’s best to view vascular disease as a whole body process and not merely limited to the heart and brain.


Communication can be understood as your whole body hormone system. It includes your thyroid system, the male or female hormone system, the hormone organs of origin (ie-adrenal and thyroid) and their connections with the nervous system. This also includes the hormones communication with cells at their cell walls and the nucleus of each cell. We are discovering the neuroendocrine system (the integrated nervous system with endocrine hormone system), neurohormonal system (the integrated nervous system with sex hormones like estrogen and testosterone) and also the neuroimmunological system (the integrated nervous system with its interactions with the immune system). This all falls under Communication.


This is mitochondrial science. The mitochondria are the nuclear power house of every cell in your body. Single cell organisms, like bacteria, won’t have a fully developed mitochondrial system and so can only exist as single cells. Humans however have a complex biochemical system that acts like an atomic reactor, breaking down nutritional compounds and capturing the energy released from the breakdown. If the system works correctly, you can have a high performance athlete; if it doesn’t, you can have someone debilitated from Chronic Fatigue Syndrome. Because energy is the basis for life, this system’s interactions with all other systems is legend. Without an understanding of bioenergetics (the science of energy production in biologic systems) it is impossible to appreciate the interconnected web of mitochondrial energy affecting any particular disease.


The transport system involves the transport of nutrition, hormones, enzymatic factors within the context of the Functional Medicine Matrix. It is difficult to discuss this matrix node without the context of all others. Hormones are transported either paracrine (cells in close proximity to other cells like in GI tract) or endocrine (across multiple domains like thyroid hormones). Energy itself can be transported intracellularly via ATP or within the body via glucose and fatty acid molecules. The immune systems can function via transcellular migration (across cells walls) or through the blood to different parts of the body. Transport attempts to uncover disconnections in the body’s natural transport systems and then to either address these issues or enhance them based on the interactions within the web of all other interconnections in the body.