Breakthrough Approach to Chronic Fatigue Recovery: Functional Medicine

A breakthrough approach to chronic fatigue and chronic fatigue syndrome recovery is the revolutionary science of Functional Medicine (FM). In FM, we focus on the individual and the unique circumstances of their illness rather than a generic diagnosis and statistical averages.

Rather than treat a diagnosis with a one-size-fits-all treatment protocol designed for the masses, we treat individual people and comprehensively address the specific root causes of their illness to achieve deep, sustainable healing. This is the essence of our approach to chronic fatigue syndrome.

First, we collect a very thorough history—these details make it clear we’re dealing with energy impairment, the crux of chronic fatigue syndrome. This information gives us clues to the many factors that are causing the energy debt.

Our 2 Key Functional Medicine Questions to Jumpstart Chronic Fatigue Recovery

We ask two simple key questions to help us sort out what’s causing the energy deficit:

  1. What must be gotten rid of to unleash vital energy?
  2. Are there unmet needs stalling energy production?

What Must Be Gotten Rid of to Unleash Vital Energy? 

This question leads us to consider the large array of potential irritants, toxins, allergens, or infectious agents that can lead to BTAM energy operating system dysfunction and symptoms of chronic fatigue syndrome. Some of these are robust and virulent and can, by themselves, cause severe fatigue and complex illness. Others are less damaging by themselves but when combined can lead to severe energy impairment.

Common Examples of Roadblocks to Energy Production that Must Be Gotten Rid of:


trauma, inflammation, food irritants, excessive mast cell activity, excesses of stress, unresolved emotional challenges, distractions


pesticides, industrial pollutants, plastics, mold toxins, heavy metals, cleaning chemicals, endotoxins from gut flora imbalances


food allergens, environmental allergens, drugs, chemicals, metals


viruses, fungi, bacteria, parasites, tick-born illness (lyme and co-infections), gut flora imbalances

Consideration should be given to all potential irritants, toxins, allergens, and infections suggested by the history and constellation of symptoms–there may be more than one.

Appropriate selection of testing can help confirm the causes that need to be treated. Work with an experienced Functional Medicine physician to help you sort this out.

Are There Unmet Needs Stalling Energy Production?

This question leads to consideration of all those elements of the BTAM energy operating system that are necessary for energy production to occur normally. These include:

  • Energy nutrients—from food (protein, fat, micronutrients, antioxidants, phytonutrients), water, air (oxygen)
  • Hormones—from the hypothalamus, pituitary, thyroid, adrenals, and gonads
  • Intact and functional immune response
  • Intact and functional gut (digestion, absorption, microbiome)
  • Sleep
  • Movement
  • Security, safety, love
  • Positive mindset (yes—how we think effects our energy!)

Powerful New Energy: Say Goodbye to the Outdated Conventional Medicine Approach

A Successful Individualized Treatment Plan Will Lead to:

  • reversal of the energy deficit;
  • resolution of the constellation of problems and symptoms that result from the energy deficit; and
  • full recovery of energy and wellbeing.

A Successful Energy Recovery Treatment Plan Includes:

  • removal of the irritants, toxins, allergens, or infections that are roadblocks to vital energy production, and
  • comprehensive support of your basic energy needs.

Not a Quick Fix

But this will only occur with a Functional Medicine systems-based comprehensive approach, not a quick-fix, symptom-based treatment plan.

One of the reasons chronic fatigue syndrome remains so pervasive in our society and so resistant to treatment is because CFS sufferers typically seek conventional medical care, which is not designed for comprehensive systematic treatment approaches to chronic complex illness.

Why Conventional Medicine Doesn’t Work for Chronic Fatigue Syndrome:

  • It focuses on the quick relief of acute symptoms, not sustainable, root-cause-level solutions for chronic problems;
  • It treats symptoms, often with toxic drugs begetting their own problems;
  • It offers only one-size-fits-all treatment protocols for a complex disorder with as many causes as sufferers;
  • It does not allow adequate time or resources for the full breadth of understanding required by this complex disorder;
  • It approaches the myriad problems of CFS in a subspecialist, organ-system fashion, not in a comprehensive way that acknowledges the inherent connection of the symptoms to a larger underlying set of problems;
  • It fails to utilize a basic systems biology framework to explain and resolve the energy depletion that is the foundation of the CFS symptom complex.

Your Chronic Fatigue Recovery Strategy: Get Started Now

First, in spite of what you may have been told before, know this:

  • There is an explanation for your suffering.
  • There is absolutely a treatment program that will work for you.
  • You can heal.

Second, distinguish those aspects of your chronic fatigue syndrome recovery you will need professional help with from what you can begin to do yourself right now:

You’ll need professional help sorting through potential underlying causes.

What Must Be Gotten Rid of to Unleash Vital Energy?

Uncover and remove irritants, toxins, allergens, and infections.

Are There Unmet Needs Stalling Energy Production?

Uncover and treat nutritional deficiencies, hormone deficiencies, non-restorative sleep, and lack of movement.

Get Started Now:

    • Organize a care team to help you.
    • Eat food that is rich in energy nutrition and low in inflammation and irritant potential.
    • Plan for enough sleep.
    • Learn relaxation techniques.
    • Remove excesses of stress, irritants, distractions, and negative energy from your environment.
    • Create a positive mindset about recovery.
    • Keep in mind that even those things you’ll likely need professional help with are part of your domain of control. Knowledge is power. Read through the following carefully and bring this information to your care providers.

Chronic Fatigue: Professional Assessment of Underlying Causes

Tests for Irritants, Toxins, Allergens, and Infections

The presence of many irritants, toxins, allergens, and infections can be deduced from a careful and thorough history. A skilled Functional Medicine physician with extensive experience in the evaluation and treatment of chronic complex illness should lead to the answers you seek.

Tests I commonly use to assess for these chronic fatigue triggers:

  •  Lyme disease and co-infection panels from a Lyme Disease specialty lab (IGeneX).
  • Markers for inflammation and immune system function: hsCRP, ESR, CBC, IL6, C4, C3, NK cell count and function, total IgA, total IgG and IgG subclasses, total IgM.
  • Tests to assess for mediators of mast cell activity (histamines, prostaglandins, tryptase).
  • Mast cell testing of biopsy specimens (CD 117 test).
  • Viral antibody titers: EBV, HSV6, CMV
  • Markers of biotoxicity: TGFBeta-1, VEGF, VIP
  • Comprehensive stool analysis with microbiome and immune markers.
  • Urine testing for mold toxins (mycotoxins) and environmental toxins.
  • Blood testing for heavy metals.
  • Blood testing for food protein IgG4 (though less reliable than simply doing an elimination diet).

Tests for Nutrient and Hormone Deficiencies

Deficiencies in the nutrients and hormones involved in energy production and transport must be addressed for full recovery from chronic fatigue syndrome.

Tests I commonly use to asses for nutrient and hormone deficiencies:

  • Urine organic acid testing.
  • Urine or plasma amino acid testing.
  • Blood oxidative stress markers.
  • Blood CBC (complete blood count) and CMP (comprehensive metabolic profile).
  • Blood fatty acid analysis.
  • Blood 25-hydroxy vitamin D level.
  • Blood homocysteine level.
  • Thyroid gland function: TSH, Free T3, Free T4, reverse T3, anti-thyroid peroxidase antibodies, anti-microsomal antibodies.
  • Adrenal gland function: early morning blood cortisol, DHEA-S, and aldosterone levels; ACTH-stimulation test; diurnal saliva cortisol levels.
  • Sex hormones: blood estradiol, progesterone, total testosterone, free testosterone, pregnenolone, sex hormone binding protein; urine hormone metabolites.
  • Hypothalamic/Pituitary function: TSH, ACTH, prolactin, ADH.

Chronic Fatigue: What You Can Do Right Now

Start Right Now to Create Your Professional Care Team

Find a Functional Medicine (FM) practitioner in your community who is experienced in the diagnosis and treatment of chronic complex illness like chronic fatigue syndrome.

In addition, you might want to include care team members who can help to relieve some of your more distressing symptoms while your FM doc helps with the big picture of your illness. These might include:

  • An acupuncturist to support energy.
  • A Functional Nutritionist to get you started on an energy food plan.
  • A physical therapist and/or chiropractor to help with muscle pain and mobility problems.
  • A mind-body psychologist to help with the emotional and spiritual issues of being chronically ill.
  • A yoga and meditation teacher who has experience working with people suffering from chronic illness.

Begin a Nutrient-Rich Energy Food Plan

I recommend my Foundational Intensive Nutrition Energy (FINE) food plan to all of my clients experiencing fatigue. It consists of energy-rich real food and is free of toxins, irritants, and foods that promote inflammation. Follow the simple guidelines found here.

If inflammation,  autoimmunity, or gut-related symptoms play a prominent role in your chronic fatigue syndrome experience, follow my Gut-Immune Restoration Intensive Nutrition (GRIN) food plan for a more aggressive approach to gut healing and reversal of inflammation.

It helps to have the support of a nutrition specialist who can individualize the plan for you and support you every step of the way as you make these important changes. Make sure they are trained in Functional Nutrition.


Movement of any kind may feel impossible when there’s no energy in the tank. While we need energy to move, we also need movement to make energy and to transport all the components of that energy through the blood to get it where it’s needed throughout the body. While there may be limits to what you can do, you must find a way to regularly move your body.

How to Move When You are Persistently Ill, Fatigued, or Debilitated:

For some the idea of moving vigorously, or at all, feels overwhelming, and perhaps impossible. No problem. We can gain energy and function by varying our postures, or adding loads in novel ways, whether you can actively move much or not. Try these:

  • Walk slowly and mindfully, in bare feet, to your tolerance level. Repeat throughout the day as you can.
  • Shift your lying position as often as possible. Challenge yourself with positions you may not normally use, such as front lying, perhaps with upper body bent up, resting on elbows—a good position to read or write for short intervals.
  • Try seated positions on the floor: cross-legged, side lying, with pillows, without pillows.
  • Try novel or non-uniform surfaces to load and stimulate body parts in new and different ways. For example, roll the bottoms of your feet out on a tennis ball, or stand/rest your feet on a pebble mat or similar textured surface.
  • Roll out all of your muscle groups on a foam roller.
  • Receive bodywork: massage, chiropractic, physical therapy. These all introduce forces that help mobilize muscles, stimulate circulation, and improve cellular energy production.

The Power of Body-Mind Movement Exercise

In addition to actual movement, consider imagining yourself moving. By actively visualizing movement, we induce neuroplastic changes in the brain (neuroplasticity is our brains’ potential to develop both structurally and functionally) that lead to enhanced physical mass, strength, and function. Athletes and musicians employ this technique to improve performance. It has also benefited people unable to move due to paralysis or neurodegenerative disorders. Actively imagining movement of the affected limb—or the entire body—leads to measurable improvements in strength and function.

Exercise: Move Your Body with Your Mind

If you are experiencing a period of enforced immobility, spend time imagining yourself performing the movement of your choice. What you imagine yourself doing will activate neuroplasticity by recruiting dormant movement-related parts of your brain, increasing blood flow to your brain, and strengthening your brain’s connections with the rest of your body.

Have a specific movement goal in mind, like hiking on your favorite trail in the woods. Be there. See yourself clearly in your mind, fully mobile and enjoying your hike. Hold onto that scene as if it is happening at this very moment and include as much detail as possible, engaging all of your senses. What are you wearing and how do those clothes feel on your body? Who are you with? Feel the breeze against your skin. Hear the leaves rustle and the birds singing. See the deer and squirrels. Smell the dirt and the flowers. Feel the uneven surface of the trail and the effort in your thighs as you climb those hills. How do you feel—what emotions are you experiencing?

Spend fifteen to twenty minutes twice daily with this active visualization practice. Include as many other scenarios as you would like to deeply activate your brain, support it as it forms new connections with the rest of your body, and improve your mobility.


Getting enough sleep of good quality is imperative for optimal energy production and recovery from chronic fatigue syndrome. We can all relate to the solace and deep comfort of a good night’s sleep, but it’s also critical for regulating key aspects of our health.

The restorative properties of sleep are:

  • Energy conservation and renewal.
  • Detoxification and cleansing of the brain.
  • Circadian rhythm regulation of hormones and energy.
  • Memory consolidation and dreaming.

What sleeping well means will vary from one person to the next.

Four simple questions to determine if you need better sleep:

  • Is it sustained long enough to meet your unique needs?
  • Is it deep enough and uninterrupted?
  • Does it align with the solar cycle of light and dark?
  • Are you waking up refreshed and restored?

If you answer no to any of these questions, you’re probably in need of a sleep tune up.

Relax, Pause, Meditate

Excesses of stress will always drive worsening of the conditions that lead to chronic fatigue. They may not be the primary cause, but they will add further stress to the body that leads to consumption of energy and demand for precious energy nutrients and hormones, further depleting an already depleted system.

Your body in its exhausted state is essentially telling you to stop and slow down. In essence, exhaustion is the pressure relief valve that has flattened you and powered you down to all but your most vital functions in the face of catastrophe or total overwhelm (regardless of the cause). Looked at in an adaptive way, chronic fatigue is what’s keeping you alive when your reserves are spent. It forces you into laser-sharp consideration of the facts of your dysfunction to mobilize the resources you need to heal.

You can profoundly assist this process by eliminating as many of the unnecessary stresses in your life as possible and working in time each day for quiet, rest, reflection, and meditation.


In times of illness and energy depletion we need our precious connections to those who love and care about us more than ever. Family, friends, co-workers, neighbors, community members—they are all important to help us feel less isolated and essential no matter how poorly we feel.

It can be highly beneficial to connect with others who have experienced profound fatigue or chronic illness, especially if they have a positive and constructive approach to illness that helps us feel uplifted and supported. There may be a chronic fatigue support group in your area or on-line that you can connect to.


Karyn Shanks MD. Heal: A Nine-Stage Roadmap to Recover Energy, Reverse Chronic Illness, and Claim the Potential of a Vibrant New You. 2019.

Karyn Shanks MD. How to Overcome Chronic Fatigue Syndrome 2019 (Expert Guide). 2019.

Karyn Shanks MD. How to Treat Chronic Fatigue with Energy Nutrition. 2019.

Institute of Medicine of the National Academies expert panel. Beyond Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Redefining an Illness. Report for Clinicians. 2015.

Find a Functional Medicine practitioner to work with: The Institute for Functional Medicine, Find a Practitioner. 2019.

Find a Functional Nutrition specialist to work with: Integrative and Functional Nutrition Academy. 2019.

Karyn Shanks MD. Foundational Intensive Nutrition Energy (FINE) Food Plan. 2018.

Karyn Shanks MD. The Gut-Immune Restoration Intensive Nutrition (GRIN) Food Plan. 2019.

Karyn Shanks MD. FINE and GRIN Food Plan Reinforcements. 2018.

Karyn Shanks MD. How to Heal Chronic Fatigue with Beautiful Natural Sleep. 2019.

Karyn Shanks MD. 13 Beautiful Natural Sleep Solutions for Chronic Fatigue. 2019.

Karyn Shanks MD. My Ten Rules for Starting a Meditation Practice. 2016.

Comprehensive Lyme disease and tick-born disease testing: IGeneX. 2019.

Functional Nutrition Testing through Nutr-Eval: Genova Diagnostics Lab. 2019.

Karyn Shanks MD. How to Heal Chronic Fatigue: Your Beautiful Energy Roadmap. 2019.

More on Chronic Fatigue Resolution:

Chronic Fatigue Table of Contents

  1. heal chronic fatigue syndrome How to Overcome Chronic Fatigue Syndrome 2019 (Expert Guide)

    Chronic fatigue syndrome--a crushing diagnosis: loss of energy, wellbeing, potential, and hope for the future. The truth is, healing is within your reach.

  2. heal chronic fatigue How to Treat Chronic Fatigue for Life (Expert Guide)

    21st century chronic fatigue breakthrough: the revolutionary science of Functional Medcine for personalized, root-cause strategies to recover vital energy.

  3. energy nutrition, heal chronic fatigue nutrition How to Treat Chronic Fatigue with Energy Nutrition (2019)

    Energy nutrition--the molecules derived from food that run all the business of making energy--is absolutely essential for chronic fatigue recovery.

  4. beautiful natural sleep, heal chronic fatigue with sleep How to Heal Chronic Fatigue with Beautiful Natural Sleep

    Sleep is powerful medicine and one of the absolute keys for sustainable resolution of chronic fatigue. We must sleep. Sleep is the boss. Here's how.

  5. beautiful natural sleep, heal chronic fatigue 13 Beautiful Natural Sleep Solutions for Chronic Fatigue

    Deep restorative sleep is powerful medicine for chronic fatigue. Learn these 13 essential practices for beautiful natural sleep and energy recovery.

  6. beautiful energy roadmap, heal chronic fatigue How to Heal Chronic Fatigue: Your Beautiful Energy Roadmap

    In this guide, you wil learn the roadmap--your beautiful energy roadmap--that will help you create and sustain the energy and potential you seek.

  7. root cause healing, Functional Medicine, Heal chronic fatigue with Functional Medicine How to Cure Chronic Fatigue at the Root Cause (2019)

    To successfully reverse the energy deficit that leads to chronic fatigue we must use the individualized, root cause-level approach of Functional Medicine.

  8. hypothyroidism treatment, hypothyroidism, root cause medicine, treat the fire, hypothyroidism, hypothyroid autoimmune syndrome, functional medicine How to Heal Thyroid Fatigue: Reclaim a Vibrant New You [Expert Guide]

    Learn how to successfully treat thyroid fatigue and thyroid autoimmune dysfunction by working with the root causes. Restore energy and optimize health.

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