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Dr. Cheney’s Basic Treatment Plan for Chronic Fatigue Syndrome

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Editor’s Note: Dr. Paul Cheney, M.D., Ph.D., is one of the world’s most recognized names in Chronic Fatigue Syndrome treatment and research. Currently practicing in Asheville, North Carolina, he has treated more than 3,000 patients with CFS from 48 states and 15 countries. Dr. Cheney has published numerous articles in peer reviewed medical journals, has lectured around the world on the subject of CFS, and is constantly pursuing research to refine his understanding of this dysfunction and develop an experimental treatment protocol for addressing it. He was a founding Director of the American Association of Chronic Fatigue Syndrome (AACFS), a professional association of scientists and clinicians. He was chosen to chair a select panel of nationally known clinicians to discuss treatment at the CFS Conference sponsored by the AACFS and Harvard Medical School in October of 1998.

The following protocol was compiled by Carol Sieverling based on published materials, a transcript of an office visit in 1998, and a transcript of a 1999 conference presentation. Please note that these recommendations are indeed generic (particularly regarding diet), and constitute a foundation that should apply to most CFS patients. However, each individual will have symptoms that require more specialized treatment, which is beyond the scope of this document. Consult with your healthcare professional before beginning any treatment plan.


· Perspective

· Basic Diet Recommendations

· Exercise

· Prescription Drugs

· Supplementation: Essentials

· Appendix


Attitudes and beliefs about one’s life and about chronic illness can be impediments to treatment. Measuring your worth by your accomplishments can result in anger and loss of ego when the ability to work is taken away or significantly reduced by CFIDS. There’s an over-representation of Type A patients in this disease. A change in belief systems is essential: a change in orientation from “doing” as a definition of yourself, to “being” as the definition of yourself. And to orient from recovery to healing. People can heal although they may not recover. And people can “be” although they do not “do.” As soon as patients orient toward “being” and healing, interestingly, they are far better able to “do,” and I think far better able to heal and recover. It’s almost as if once they turn away from their goal, and march off in a different direction, they actually have a better chance of getting back to the goal they turned away from.

Conversely, if they’re going to “do” no matter what and recovery is their absolute goal, I don’t think they do that well. Similarly destructive beliefs are those such as hopelessness about the possibility for improvement, or an attitude that “my illness allows me to control others.” Acceptance of one’s illness and finding new ways to view oneself as a contributing member of society are critical to setting the stage for medical treatment. Two tapes are recommended to patients: “The Power of Myth” by Joseph Campbell with Bill Moyers, and “Why People Don’t Heal and How They Can” by Carolyn Myss. (Editor’s Note: These tapes can be purchased from www.Amazon.com).


NO SUGAR: Due to defects in utilization, it produces toxins that cause pain, headaches and neuro-psychiatric problems. Sugar stimulates the growth of abnormal gut microflora, especially candida. It generates a tremendous amount of free radicals and raises insulin levels, both very problematic. If you crave it, try eating carbohydrates instead. If you must, eat sugar (including fruit) with meals, never alone. Some honey and powdered fructose can be used in cooking, as well as the herb stevia.

REDUCE “BAD” FAT: Limit daily intake to less than 30 grams due to a defect in fat transport across mitochondrial membrane. Supplementation, however, of essential fats (EFA’s omega 3 and 6) is necessary.

NO NUTRI-SWEET: It contains the toxin methanol and can exacerbate neurotoxicity.

NO RED MEAT: High in bad fat & difficult to digest, causing GI tract symptoms & systemic symptoms such as joint pain.

NO CAFFEINE: or at least limit it as much as possible.

BE CAREFUL WITH THE FOLLOWING: Eliminate them entirely or try two, separate, three week programs of off/on/off these foods and note if symptoms improve in the off week.

· Dairy products (can cause GI and systemic symptoms)

· Gluten (can cause GI and systemic symptoms) It’s found in wheat and oats, and thus in cereal, bread and pasta. Gluten free products are available.


The single most common antigen to which we are exposed is food proteins. If food protein is not properly digested, it’s a significant inducer of immune activation in the gut, and it can maintain this disease indefinitely. Put another way, as long as you eat indiscriminately, you cannot get well with chronic fatigue syndrome. So ultimately you have to begin a process of determining the foods to which you are reacting, and eliminate them. Perhaps more important is to digest the food in the first place, which I don’t think patients do very well. They then get undigested food protein coursing through the small bowel.

There are permeability issues that affect the gut. If the gut is permeable, nothing digests completely and the undigested food particles course across the boundary into the bloodstream and get exposed to immune cells that perceive them as foreign bodies and trigger an allergic response and then you’re off to the races with this disease. So I think a lot of attention to elimination diets, and improving digestion and gut epithelial function can pay huge dividends in this patient population. I’ve seen people in 30 days have huge clinical responses simply by this very simplest of moves.

(Editor’s note: Dr. Cheney uses the ALCAT test to determine food sensitivities, most of which are temporary, and he is now using bioenergetic testing as well. This is also sometimes referred to as electrodermal testing.)


Golden Rule: Find the boundaries of what you can do and then stay within them. Both trying to do too much, or pulling back and doing too little are counter productive. Limit setting is probably the most important thing you can do. Patients are very susceptible to push-crash phenomena and you need to learn to stay within certain boundaries. To the extent you do that, you will tend to do better. To the extent you don’t, you likely will not do well.

Aerobic Training: Beyond certain limits this cannot be attempted until you are much improved. Be cautious about any aerobic exercise (any sustained activity, such as running, walking, or swimming, designed to raise the heart rate and increase oxygen flow throughout the body). The aerobic system is injured and reactive oxygen species (free radicals) generated in the mitochondria by excessive training may not be detoxified with resulting injury which can potentially be permanent (DNA damage). Walk, cycle or swim only as much as your body will allow, no more than 20 minutes, three times per week. Aerobic exercise past a certain point can dramatically worsen this disorder.

Anaerobic Training: The anaerobic pathway is largely intact in CFIDS. Weightlifting, isometrics, and stretching can maintain muscle tone and strength and improve the elimination of toxins formed by the pathway itself. Do low level weight lifting with 1 to 20 pounds, using all muscle groups. Lift for 10 seconds, rest for 60 seconds – repeat for each muscle group. Do lift/rest cycles no more than 20 minutes three times per week. Sequential isometric contractions can be substituted for weight lifting. (This can be done while lying down.) Still use the 10 seconds on and 60 seconds off rule.

Rebound Exercise: The bounce-back chair (a tall bungee cord-like contraption) is probably the best form of exercise for CFIDS. Low level, non-vigorous bouncing for ten to fifteen minutes every other day is best.

Less ill patients can add aerobic exercises between five-minute periods of bouncing per the videotape instructions. Its advantages include correcting dysautonmia, the dysfunction of the autonomic nervous system that underlies many of the symptoms in CFIDS. The Bounce Back Chair was studied by NASA to treat astronauts returning from orbit who fainted upon standing. After six months in orbit, you lose your autonomic nervous system capacity to stand in a gravitational field. You simply faint and seize. If you remember these astronauts, when they took them out of the capsule they had to drag them out vertically because they would faint on standing. They end up with a dysautonomic condition similar to chronic fatigue syndrome patients.

NASA figured out that the best way to bring back the autonomic nerve system was to bounce. So they put them in these bungee cord contraptions and they just bounced them–this up and down motion essentially regulates autonomic tone and improves the autonomic nervous system. Rebound exercise is very easy, it’s non-weight bearing, and you can add in arms, legs and abdominal motion while bouncing, to tolerance. It also improves immune regulation by pumping lymphatic fluid back into the blood. Lymph acts just like gamma globulin. Finally, this exercise was shown by NASA to be 68% more efficient as an exercise routine than running. (“Efficient” means maximum gain for minimum effort.) It is therefore ideal for people with little energy to spare. Those who do not suffer from balance problems can achieve many of the same benefits from a mini-trampoline.


Klonopin (generic: clonazepam) (0.5mg): This is a long acting benzodiazepine, and my most effective drug over the years. It can improve sleep and reduce NMDA receptor mediated neurotoxicity (see The CFIDS Chronicle, Summer 1995, page 38). The injured brain fires at lower stimuli, resulting in increased sensitivity to light and noise, as well as pain amplification. Klonopin and magnesium raise the sensitivity threshold, blocking this brain response, and may be two of the most important treatments for patients. Recommended dosage is 2 or more tablets at night.

Paradoxically, very small doses (usually a quarter to a half a tablet in the morning and mid-afternoon) improve cognitive function and energy. If the daytime dose is low enough, patients will actually get a lot clearer and think better. If the daytime dose is too high patients will become drowsy. Patients need to adjust their dose for maximum benefit. Adjust the morning dose first, then take the same amount mid-afternoon if needed, then take three to four times the morning dose at bedtime. Consider doubling the dose during severe relapses.

Doxepin Elixir (10mg/ml): At low doses this tricyclic anti-depressant acts as a very potent antihistamine and immune modulator. I suspect it’s the most powerful antihistamine known to man and gets into the central nervous system. I think it adjusts the histamine receptors, which are the grand maestro of the central nervous system, and down regulates it, which is beneficial. It acts synergistically with Klonopin for sleep and may improve pain. Patients are very sensitive to Doxepin, which can cause morning fog and fatigue if the dose is too high (5 to 10 mg. or higher). I recommend starting at two drops a night and advancing for sleep improvement vs. morning fog, up to half a cc. Elavil may prove more beneficial for some (10 to 75 mg at bedtime).

Kutapressin is a broad-spectrum anti-viral. I prescribe it for those who test positive for a reactivated virus: EBV, CMV, HHV6, etc. Benefits may not peak until four months or longer. Daily sub-Q doses of 2cc or greater seem to work best.

B-12 Injections (10,000 mcg/ml of hydroxycobalamin, 1cc or more daily, given subcutaneously or intramuscularly.) This form and dosage of B-12 is a potent detoxifier, increases energy, may assist with sleep if taken at bedtime, and provides pain relief for some. When using B-12 as a detoxifier high doses are needed–at least as many B-12 molecules as there are toxins. It’s brain specific. And two-thirds of CFS patients have no detectable B-12 in their brains, even though blood levels are normal.

B-12 is highly compartmentalized, so levels could be normal in the blood but absent in the brain. I believe it is absent because it is being coupled to toxins – neurotoxins, probably xenobiotics, because B-12 couples to nitrogen. Nitrogenous waste molecules in the brain are coupling out the B-12 as fast as it’s leaking in, and you end up with no B-12 in the brain. The British used 5 gm infusions of hydroxycobalamin to successfully detox people with cyanide poisoning.

Another study documents the use of up to 26 mg a day of B-12 with great benefits and no side effects. At these high doses hydroxycobalamin rather than cyanocobalamin must be used to avoid the toxicity of the cyanide in the later. To the extent that cyanocobalamin might be a good detoxifier, which it isn’t, you just trade cyanide for the toxin it removes. A few patients have reported feeling hyper/jittery or lethargic, or experience acne and diarrhea when taking the hydroxycobalamin. Reduce the dose if this occurs – it’s pulling out toxins too fast.

It’s important to supplement other B vitamins moderately when taking high dosages of B-12. This form of B-12 is available only through a compounding pharmacy. Hydroxycobalamin is heat sensitive, so be sure to refrigerate it. See appendix for abstracts of the three studies referred to in this paragraph.


Magnesium is extremely important. It prevents neurotoxicity (see Klonopin), improves energy, helps sleep, and reduces muscle pain. I strongly recommend magnesium glycinate, which is magnesium chelated to glycine, the smallest amino acid. It has superior bioavailability and transports well across the blood brain barrier and into cells. Oral magnesium, especially if not in the glycinate form, can cause diarrhea. Reduce dose if this occurs. 200 to 500 mg a day.

Multi-vitamin: A good multi-vitamin with selenium and without iron or copper is essential. Iron and copper increase oxidative stress (free radical damage), which is a major problem in CFIDS. Unless you test low in iron, get a multi without it.

Reduced L-Glutathione: Glutathione plays a major role in the body’s detoxification pathways and in its viral repression mechanisms. It is also a very potent anti-oxidant (counteracts free radical damage/oxidative stress/reactive oxygen species). Most CFIDS patients show significant glutathione deficiency. Many patients notice improvement in headaches with this supplement. Always take it with food. The dosage range is 500 to 800 mg. a day. Start low then increase. Use higher doses during relapses if symptoms are improved on high doses.

Rare patients will not do well on glutathione and it should be stopped in those patients.

Coenzyme Q10 (CoQ10) is a co-factor in mitochondrial production of ATP (cellular energy). It is also a powerful anti-oxidant and critical in the protection of DNA. It can influence fatigue, muscle function, and perhaps cognition. In terms of dose, I think the more the better, but realistically 200 mg. We tend to use it crunched under the tongue since it’s not very well absorbed, although there are other absorbable forms that can be swallowed.

Lipoic Acid is a powerful anti-oxidant and helps protect the brain. It may be one of the most important supplements, particularly for the central nervous system. 100 to 300 mg. daily.

Essential Fatty Acids (EFA’s) are very important in cell membrane and immune function and intracellular regulation of the inflammatory process. They can help regulate menses and reduce PMS. Testing reveals that most patients are low in EFA’s to begin with, and a low-fat diet places one at even greater risk. Omega 3 EFA’s are found in DEPA (marine lipid concentrate) capsules or Flaxseed Oil Capsules. Omega 6 EFA’s are found in Ultra G.L.A. (borage oil) capsules. If in doubt, red blood cell EFA testing can determine exactly what you need.

Probiotics are essential in replacing the healthy microflora of the intestinal tract that are killed off as the unhealthy microflora, bacteria, parasites, yeast, etc. multiply and set up the intestinal permeability that causes so many systemic problems. A good product will contain acidophilus, bifidus, bifidum, rhamnosus, etc. Around 10 billion organisms is a good daily dose. Though important at any time, it is critical to take probiotics if you are taking antibiotics.

NOTE: Antioxidants are especially important even though you may not notice any significant improvement in current symptoms. I believe they can prevent permanent damage caused by free radicals (oxidative stress) and increase the possibilities of a good recovery in the future.



Plant bioflavonoids are very important. If you just use multi-vitamins, you don’t get much improvement in lipid peroxidation until you add in the plant bioflavonoids, which I think act to couple, oxidize and reduce these vitamins. Otherwise, the vitamins don’t work very well. Examples of plant bioflavonoids are proanthocyanadins, pycnogenol®, silymarin, quercetin, ginkgo biloba, green tea, grape seed extract, and many others. Bioflavanoids not only augment the effects of antioxidants by recycling them to their reduced state, they also reduce the chance of a pro-oxidant effect (oxidative stress/free radical damage). Pycnogenol® has a particularly potent effect in the brain, and silymarin in the liver.

Vitamin C: Take 2000 to 4000 mg. in addition to your multi-vitamin. Take mega doses (10 to 20 gms) with caution: they can actually cause a glutathione deficiency (with a resulting crash) and in some patients augment feriton chemistry injury by iron.

Vitamin E: Take 400 to 800 IUs, preferably unesterified. Most patients are deficient in E. Activated vitamin B-6 is recommended to treat the B-6 deficiency in the brain which is evident in many patients. This supplement is also important if you are taking the very high doses of B-12 that are recommended. 50 to 100 mg a day are recommended, in addition to the multi-vitamin.

Digestive Enzymes can greatly improve digestion and improve gut ecology and function. They will also improve energy, since they assist with energy intensive digestion, allowing more energy for other uses. One to three caps with each meal are recommended. Some patients respond best to animal enzymes, others to plant enzymes. Only trial and error can determine which is best.

Betaine HCL is important to add to certain acid dependent digestive enzymes so that they work better. Too much causes diarrhea and too little causes reflux heartburn.


I believe that the glutathione deficiency found in virtually all patients is the key problem, particularly over time. Nothing we’ve tried has significantly increasing its functionality. The consistent low to low-normal levels of glutathione in whole blood, and particularly the abnormal functional markers of glutathione (elevated lipid peroxides, elevated citrate, depressed alpha ketogluterate) indicated that neither supplementation, injections, nor other interventions seemed to be addressing intracellular levels, which is where 90% of the body’s glutathione is needed. The deficiency has been extremely treatment resistant.

There are two major implications of glutathione deficiency: detox failure and viral/microbial activation. Glutathione plays a major role in the detoxification pathways of the body. This deficiency impairs the body’s ability to get rid of toxins, whether environmental or by-products of cellular metabolism. CFS patients slowly become toxic, storing away poisons in fatty tissues, muscles, organs, and brain. The cellular detox failure this deficiency causes can make these patients canaries to their environment. Detox programs that have been successful in other conditions can actually put some CFS patients in the hospital if their glutathione deficiency is not first addressed.

Glutathione is also a powerful antiviral and antimicrobial weapon. The glutathione deficiency not only compromises our antiviral/antimicrobial defenses, but it also has a potent pro-viral effect. That is, not only does glutathione tend to act as an anti-viral, but glutathione deficiency also produces a pro-viral effect. It can actually augment viral replication. Given the widespread activation of viruses like EBV, CMV, and HHV6, and the activation of microbes like mycoplasma, chlamydia pneumoniae and candida in CFIDS, finding a way to raise intracellular levels of glutathione has been a top priority at out clinic. If you raise the glutathione levels you can stop the replication of most any intracellular pathogen. We believe we have found a way to do this – undenatured whey protein. We conducted a six month study using the first patented bioactive whey product and discovered that it improved glutathione functionality significantly.

CONTACT INFORMATION: Due to illness, Dr. Cheney is not practicing as of 2004.

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3 thoughts on “Dr. Cheney’s Basic Treatment Plan for Chronic Fatigue Syndrome”

  1. jortatum says:

    Dr. Cheney recommended something that we use for increasing glutathione! It has helped You can PM me if you like. Joanne Tatum

  2. youlie says:

    With God all things are possible.

    1. youlie says:

      Yes in that cfids patient can overdo without being aware at the time.

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