CISRA’s Synergy Health Newsletter

Issue 10. Improvement on the Marshall Protocol: Data and Case Histories (2007)

by J. C. Waterhouse, Ph.D.

Cautions, Comparisons With Other Protocols

It should be noted that although the following case reports are very encouraging, not everyone does this well on the Marshall Protocol (MP), especially in the first year. Sometimes, prior to beginning the MP, a patient has been on immunosuppressive drugs or supplements (eg., high dose vitamin D), which may have made them feel less ill than they really are, while allowing the bacteria to increase unhampered.

The Marshall Protocol decreases high 25D levels and activates bacterial killing, which may initially increase symptoms. Occasionally, excessive immune system reactions (Jarisch-Herxheimer, “Herx” or bacterial “die-off”) reactions can begin with the MP and can be difficult to stop, due to the immune system finally becoming active and attacking the CWD bacteria. In most cases, variation in the MP medications and/or palliative medicines can be used to control these “runaway Herxes” that occur in some patients. In a very few cases, a steroid medication (dexamethasone) is resorted to in order to stop these “runaway Herxes” (2008 note – this is no longer recommended). It should be remembered, though, that during these reactions, it appears that bacteria are being killed at a high rate, so one is still healing during the “runaway” reaction.

It is important to go at your own pace, since some need to go slower, especially if they have been sick a long time. It is also essential that both doctors and patients study the protocol carefully, since serious and even life-threatening reactions can occur if one does not follow cautiously follow the guidelines from the MP site. It is also helpful for patients and doctors to read other patients’ progress reports so as to understand the MP as thoroughly as possible before beginning it. Health care professionals are encouraged to join the private forum for medical professionals (

It also should be noted that although many patients feel better on Benicar as it is used in the MP, a few patients seem to have difficult tolerating it. Sometimes this may due to having a very high bacterial load and there are various strategies that can help in this situation that are described on the MP site. Another possible reason for difficulty tolerating Benicar that may play a role in a small minority of people prone to food/drug intolerances is discussed in this article).

However, it should be noted that there are various other antibacterial protocols currently in use that do not involve Benicar. I do not have information on their success rates, but examples of these alternatives are the antibiotic protocol used by the Roadback Foundation for rheumatoid arthritis, ( and, another approach developed by Dr. Wheldon for Multiple Sclerosis (, and various protocols used by ILADS for Lyme disease and autoimmune illnesses ( and

Other protocols have drawbacks and some may be expensive, ineffective, only partially effective, palliative or only give short term benefits (eg, they use antibiotics that only kill organisms with cell walls, like Rocephin, bicillin and amoxicillin) in addition to lacking the organ protective effects provided by Benicar. Unlike the MP, protocols that use high antibiotic dosage levels often lead to Candida (yeast) overgrowth and may damage organs like the liver or gallbladder. Higher doses of antibiotics used in these approaches can cause overgrowth of pathogenic intestinal bacteria that may have long-term negative consequences, as well (e.g., Klebsiella and other members of the Enterobacteriaceae, see Issue 10 article on CGA Sensitivity, VBS-Producing Bacteria). These protocols can also produce excessive and long lasting Jarisch-Herxheimer reactions, at times, and so must also be used with caution.

Some doctors and patients using the above non MP protocols have very recently begun promoting high vitamin D intakes. According to Dr. Marshall’s research and new molecular modeling, it appears that this can cause short-term symptoms reduction at the expense of long term healing. Vitamin D supplementation was not an original part of these protocols and thus could be having detrimental effects on their long term outcomes, while appearing to be helpful initially.

The following excerpt is from Waterhouse, J.C., The Marshall Protocol for Lyme disease and other chronic inflammatory conditions. The Townsend Letter for Doctors and Patients 2007; Two-part article, April and May 2007 issues; No. 285 and No. 286.
Part One:
Part Two:


Preliminary results for chronic Lyme disease patients show that of the 51 patients who have been followed on the protocol study site for 6 – 22 months, 29 are reporting tangible improvement.

Marshall also finds significant improvement rates in various other chronic diseases (Table 1). These results probably underestimate the ultimate efficacy of the treatment because many patients were still in fairly early stages of treatment and were still undergoing strong immunopathology responses to bacterial killing (a.k.a. Jarisch Herxheimer Reactions).

Table 1: Number of Patients / Numbers Reporting Improvement

Rheumatoid Arthritis 8 / 7

Hashimoto’s Thyroiditis 25 / 20

Osteoarthritis 5 / 4

Chronic Fatigue Syndrome CFS/ME 77 / 40

Cardiac Arrhythmia 15 / 9

Sarcoidosis 92 / 57

Type II Diabetes 5 / 3

Uveitis 18 / 12

Fibromyalgia 34 / 20

Irritable Bowel Syndrome 10 / 8

Brief Case Histories

Patient 1 is a 14-year-old boy who has been ill with chronic Lyme Disease (with Rickettsial and Chlamydial coinfections) since June 2004. He suffered from chronic severe headaches, debilitating fatigue, a tourette-like tic occurring every few seconds, blurred/double vision, photophobia, nausea, vertigo, insomnia and visual tracking problems that prevented him from reading or writing. After 16 months on the MP, all of his symptoms have greatly improved, and his tic and visual problems have completely disappeared. He is now able to resume most of his previous activities and continues to improve on the protocol.

Patient 2 is a 58-year-old woman who was diagnosed with Lyme disease in 1999. She had been treated with oral doxycycline in 1999 and 2001. She relapsed after having begun extra vitamin D supplements and increasing sun exposure. Many symptoms have greatly improved in the 29 months since she began the MP, including muscle pain, stiffness and weakness, fatigue, headaches, panic attacks, colitis attacks, nausea, bloating, indigestion and insomnia. She reports that on the MP, her low back pain has gone from a level 8 to a level 1 on a 10-point scale (attributed to bulging discs at L4 and L5 on MRI), despite decreasing her use of pain medication.

Patient 3 is a 55-year-old female who was diagnosed with rheumatoid arthritis 10 years ago. She had previously been on high dose antibiotics (mostly oral, with some IV and IM) for 6 years prior to the MP and had minimal improvement. Her condition worsened while taking vitamin D prior to the MP (800 to 2400 IU daily over a 2 year period). After 29 months on the MP, she reports reduced pain medication use, significantly greater strength and less pain in her hands and upper body and less fatigue. Recently, her ANA (anti nuclear antibody) tested negative, after having all 17 prior tests showing elevated levels (usually 1:640 or more).

Patient 4 is a 42-year-old man diagnosed with chronic fatigue syndrome and fibromyalgia. His illness began after he became ill with infectious mononucleosis at the age of 22. Prior to beginning the MP, he could only work 2 or 3 days per week and had adverse consequences for days following exercise. He began the MP in March of 2005, and since then he has had 90-100% resolution of his headaches, light sensitivity, tinnitus, sinus congestion, sore throat, unrefreshing sleep, swelling of fingers and feet, fibromyalgia and heart palpitations. He has had 70-75% resolution of brain fog, fatigue and lymph node swelling. He still requires injections of IgG due to a deficiency of IgG3, but the injection interval has increased from an average of 14 days to more than 24 days since commencing the MP. After 22 months on the protocol, he reports feeling markedly better than anytime in the last 20 years and is able to work full time and perform strenuous physical activity.

Patient 5 is a 43-year-old man who had psoriasis since the age of 7, chronic insomnia beginning at the age of 26 and sarcoidosis, diagnosed at the age of 36. His wife had been diagnosed with sarcoidosis several years before. This is in accord with the familial tendency that has been observed among Th1 diseases due to spread of the bacteria among family members. Prior to the MP, numerous treatments had failed to help his psoriasis (e.g., PUVA, steroids, fish liver oil). In contrast, while on the MP, the psoriasis went from 70% coverage of his skin to 1%. The insomnia resolved completely soon after the Benicar was begun. The patient had also suffered from chronic kidney stones, which ceased when he began the protocol. Treatment with the MP has resulted in more than 95% resolution of his symptoms of sarcoidosis (coughing, fatigue, sinusitis, memory problems, muscle aches etc…), and his chest x-ray is now normal as he continues his fourth year of the MP.

Patient 6 is a 48-year-old woman who was diagnosed with sarcoidosis in 1991. In 1998, she developed seasonal affective disorder (SAD) and began taking anti-depressants every winter to treat the depression. After beginning the MP in October of 2006, she found she was not depressed and did not need her anti-depressant. The combination of 40 mg Benicar every 6 hours and avoiding vitamin D was sufficient to relieve her SAD (she wears a zinc oxide containing sunscreen to help minimize vitamin D production and NoIR sunglasses). She has only been on the MP for a few months, but finds her fatigue has significantly lessened.

Patient 7 is a 61-year-old woman with presumed sarcoidosis (based on CT scan), with unilateral tibial neuropathy presenting with altered sensation, severe foot atrophy and calf muscle cramps. So far on the MP, she has regained 95% of her muscle tone, strength and mobility in her foot and leg. Her fatigue, depression and cutaneous lesions also resolved. Two other examples of severe neurosarcoidosis showing marked improvement on the MP are described elsewhere (3).

Patient 8 is a 67 year-old man who has had sarcoidosis of multiple organs, including the heart and lungs, for over 20 years. He had a pacemaker implanted in 1995 and has undergone two quadruple bypasses. He had been in atrial fibrillation over 90% of the time in the two years prior to the MP. After 3 months of treatment with the MP, with no other changes in medication, his atrial fibrillation disappeared and has not returned in the following 20 months. His chest x-rays have improved significantly and his shortness of breath and fatigue have also improved as he continues on the MP.

Patient 9 is a 51-year-old woman who has been diagnosed with numerous conditions over many years of being ill. Since beginning the Marshall Protocol, her symptoms of Lyme disease (muscle/joint pain, fatigue, cognitive problems) and her Sjogren’s syndrome and Raynaud’s symptoms have significantly improved. Her myasthenia gravis, diabetes insipidus, gastroesophageal reflux disease, Barrett’s esophagus, interstitial cystitis, allergies, multiple chemical sensitivity, and migraines have greatly improved and her chronic yeast infections (vaginal and esophageal) have completely resolved. She can now read, use the computer, drive a car and walk without a cane, things she could not do before the MP.

Editorial Note (2008): see video and chart below for additional data for 20 Autoimmune diseases, fibromyalgia and chronic fatigue syndrome —

Waterhouse JC, Perez TH, Albert P, Proal A, Presentation. Bacteria-induced vitamin D receptor dysfunction in autoimmune disease: theoretical and practical implications for interpretation of serum vitamin D metabolite levels, International Congress on Autoimmunity, Porto, Portugal, 2008, (video:, data:

Written by synergyhn

August 28, 2007 at 1:19 am

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