CISRA’s Synergy Health Newsletter

Issue 9. My Progress on the Marshall Protocol — Going Slowly to Achieve Success (2007)

by J.C. Waterhouse, Ph.D.

Don’t Try to Rush the Marshall Protocol

I believe the cardinal rule for those who go on the Marshall Protocol (MP) is, if in doubt, choose the more cautious option and never try to rush the MP. Trying to do the MP at a faster pace than your body can handle may cause you to feel quite ill all the time and may lead to a situation where it takes quite some time to get over a “runaway Herx.” “Herx” is short for Jarisch-Herxheimer Reaction, a type of immunopathology which occurs when one’s immune system reacts to and clears up the bacterial debris and dead cells that result from the bacteria being killed, producing an exacerbation of symptoms. The terms immune reaction or immunopathology are now beginning to replace the use of the term “Herx.” A number of people have discovered that trying to speed up the MP ended up actually slowing them down (see, “I’m eager to get well…”

Focus enough on the MP to follow it correctly, but don’t focus on it to the exclusion of everything else, or this may tend to make you want to hurry it too much. Keep or develop other interests that you can pursue while on the MP. One example of something that you can do while resting that has helped me greatly is listening to free books on tape, available to those who are ill. You can obtain an extremely wide variety of books, including textbooks for all grades, up through graduate and medical school, as well as books for entertainment ( The support of other patients on the MP site is also very helpful to keep one on track and so I highly recommend that you participate in this free online community (see

Some General Cautions

If you are taking thyroid medication or the drug, lithium, your doctor should be sure to monitor your blood levels with the appropriate tests when on the MP. People often find they need less thyroid when on the MP and so if they don’t monitor their thyroid levels and adjust their thyroid medications, they may become hyperthyroid. One should generally not supplement with potassium when using Benicar, since Benicar may cause a tendency to retain potassium (Note: potassium is also found in Sports Drinks and certain other alkalinizing drinks and so these should be avoided too). Monitoring potassium may be a good idea for patients on the MP. The MP should not be used when pregnant or breast feeding. There are other medications and supplements that should be avoided (see

One should generally be very careful regarding the use of massage when on the MP. Some patients who had deep massage had a large increase in Herx that caused them problems. Taking very hot baths or saunas or doing exercises that raise your body temperature may also increase the Herx. These things may have been appropriate when on other antibiotics, that were not very effective, but the MP is so effective, that one must be more careful using these other modalities –they can result in too much Herxing sometimes.

There are a number of options to adjust the level of Herx involving changes in Benicar and/or antibiotic doses (see “My Herx is too strong” Many find reducing or delaying the minocycline dose to be most helpful. For other people, under certain circumstances, taking minocycline at a more constant and somewhat higher dose reduces the Herx, if it gets to be too strong. This is due to well documented anti-inflammatory properties of minocycline. But it doesn’t work equally well for everyone. Sometimes switching to a different antibiotic combination may be helpful. There is also a new Herx reduction approach that your doctor can ask Dr. Marshall or his staff about or consult the private forum for health professionals within the Marshall Protocol web site.

At the time I began the Marshall Protocol (MP), in October, 2004, a number of people with Lyme disease and chronic fatigue syndrome were starting at very low doses of minocycline and increasing at smaller increments because of noticing that some people were having trouble starting at 25 mg. Though, not all did equally well, I did fine starting at a very low dose and increasing quite gradually, and a number of others did quite well too. It should be noted that the current recommended guidelines for the MP give the starting dose as 25 mg minocycline and lower starting doses are discouraged. There are other methods currently used to help control Herxing that Dr. Marshall and his staff believe to be better, on the whole, than the very low starting doses (for a more complete account of my experiences, see

This article is just meant to describe my experience and point out some cautions and give some tips. I suggest that you still study the Marshall Protocol web site for at least several weeks before starting the MP to become thoroughly familiar with it (for more information, see and

My Progress: Beginning the MP

Before beginning minocycline, I had already experienced some improvement from ceasing vitamin D supplementation and reducing sun/bright light exposure for several weeks. I had some improvement in sleep, endurance, energy levels, strength and cognitive abilities. I had a few mild symptom increases when I began Benicar at 160 mg daily. I think the Benicar, through lowering 1,25D, helped my body more effectively excrete phosphate (which a previous treatment, guaifenesin, had also done). Elevated 1,25D is known to cause phosphate retention. I also think I began to have some bacterial die-off reaction (Jarisch-Herxheimer reaction or “Herx”), confirming that Benicar alone does have some antibacterial effect, just as Dr. Marshall has observed (for details, see

But the symptom increases related to Benicar were quite mild and declined over time, so after being on Benicar for two weeks, I began minocycline at 3 mg. I began taking brand name Minocin, which I find to have a stronger effect on me than generic minocycline, probably due to better absorption. So, the brand name Minocin may have been more equivalent to 4 or 5 mg of generic minocycline. Though tolerable, it was the strongest Herx I had ever had (despite having previously taken many oral antibiotics and antibiotic combinations before the MP). Because it was a pretty strong reaction, I decided to wait several days before taking another dose and decided to cut back to 1.5 mg for a couple doses.

I then worked my way up, usually at 3 mg intervals to 12.5 mg. From that point on, I usually increased by 12.5 mg intervals. I spent quite a while at doses of 50 mg and below. For instance, I spent 3 weeks at 37.5 mg and took almost 3 months to reach 50 mg. I took a total of 4 ½ months to finish phase one. I did not worry if I spent a long time at a particular dose. As long as I was Herxing tolerably, that was fine. I gave myself breaks now and then by extending the interval between doses, particularly at times I needed to minimize symptoms to better accomplish things I needed to do. I was very strictly compliant with regard to light exposure and vitamin D. Eventually, ketoconazole cream became available, which made it easier when I needed to go out in the daytime. I used it on my face and hands when I needed to be outside. It is known to block the conversion of the precursor 25D to the active steroid hormone form of vitamin D (1,25D). Recently, some MP patients have found that translucent zinc oxide sunscreens also help reduce sun exposure symptoms. An ongoing study of various zinc oxide containing sunscreens on the Marshall Protocol site should be consulted for more information. These options allow most people more flexibility with regard to sun exposure than was previously possible on the MP.

Although I went at a fairly slow pace, I think I would have had to go even slower if I had not already reduced my severe food allergies/sensitivities (see articles in Issues 5 and Issue 10) and my susceptibility to colds and flus ( I think I was also helped by previously having taken guaifenesin ( — Note: I no longer take guaifenesin) and magnesium glycinate ( My two years of pre MP antibiotics for Lyme Disease, though not causing noticeable improvement, probably reduced my bacterial load to some degree and may have allowed me to improve more rapidly than some people. Although I had some improvement fairly early in the protocol, some people do not notice improvement until 9-12 months or longer on the MP.

Modified Phase Two

I chose the modified Phase Two instead of the regular Phase Two largely because of the shorter time that the modified Phase Two antibiotic stays in one’s system relative to the regular Phase Two antibiotic. The shorter time means the Herxes are usually more manageable. The modified Phase Two is also preferred for patients with cardiac involvement and in any other case where the regular Phase Two has been found to be difficult. However, this antibiotic combination may not be tolerated as well by someone who has severe problems with depression or other neurological symptoms. If you fit this category, even greater caution must be used with this combination and sometimes it is suggested that another combination be used first.

The reason the Phase Two antibiotics are not named here is that when they are added, the Herx can be quite strong and possibly even life threatening if one does not understand and carefully follow the MP. So, although a doctor can obtain the Phase Two and Three protocols at any time upon request, patients are asked to fill out a questionnaire on the web site first, to show they understand and are complying with the MP, before they are given free access to the Phase Two and Three protocols and the corresponding section of the MP web site. Patients who know about these antibiotics are asked to keep the Phase Two and Three antibiotics private to help in this effort to protect newer patients.

I began the modified Phase Two at ¼ of a 150 mg capsule of the new antibiotic and 100 mg minocycline every other day. Looking back, I feel it would have been more cautious to begin at 1/8 of the new antibiotic and 25 mg minocycline. I usually increased by 1/8 of a capsule of the new antibiotic each time it was time to increase (when the Herx had declined to a minimal level), rather than by the usual ¼. The modified Phase Two combination often tends to have a cumulative effect, so I found that a 3 or 4 day cycle often was more tolerable than a 2 day cycle (QOD, which means every other day dosing). Some patients use other strategies if the immune reaction to bacterial killing becomes too strong. For instance, some people only take the second antibiotic every 4th day, while still taking the minocycline every other day. The green capsules contained a dye that many people may not tolerate, so it is probably better to divide up doses and transfer contents into clear gelatin capsules (they can be bought at a health food store or ordered from a place like 1-800-634-1380). Some people on the MP prefer to have a compounding pharmacy prepare capsules at the needed dose levels, while others divide up the capsules or tablets themselves.

I had strong manageable Herxing throughout my time on Phase Two. Each time I increased the new antibiotic by 1/8 of a 150 mg capsule, I got a significant increase in Herx that included a lot of fatigue. With the first dose at a given level, I usually also had disrupted sleep and some diarrhea, along with negative/anxious dreams and a greater tendency to anxiety and depression when awake. It was quite remarkable how well this antibiotic combination seemed to be affecting CWD bacteria in the brain, as evidenced by the type of Herx symptoms I experienced. Many other patients note this effect from the modified Phase Two. I also had a little light headedness now and then, and some teeth/gum pain, along with deep pelvic/inguinal/psoas and varied other pains. Over time, the Herx reactions on a particular dose level waned and I gradually experienced less intense symptoms.

I would increase the minocycline by increments of 25 mg each time, but would only increase one antibiotic at a time. There were several times when the fatigue and depressive symptoms seemed too strong and I reduced the dose of antibiotics. I reduced minocycline from 100 mg to 50 mg at one point, and at another point, I reduced the dose of the second antibiotic from ½ to 3/8 of a capsule.

Several months into Phase Two, I decided to take a break from the MP for a few weeks. This was for several reasons. One was that I wanted to do a trial of another drug as an experimental treatment. Another reason was that I thought I was becoming sensitive to Benicar. This did turn out to be the case, based on pulse testing and symptom changes, but I found the sensitivity was not high and by taking a break, it helped the sensitivity to decline quickly. After the break, the Benicar sensitivity was gone and although it appeared again at one point, it now seems to be almost entirely gone.

I think the break I took was also helpful in my case, because I had been trying to take the antibiotics every 2 days for a couple weeks and their cumulative effect had begun to make me feel more consistently depressed. Taking a break helped that, though a shorter break, or a switch from taking the antibiotics every second day to every 3 to 5 days would also have probably been adequate to correct this problem.

During the break, I also changed my diet temporarily. I have very extensive food allergies/sensitivities and my sensitivity to my usual hypoallergenic diet of white rice and skinless chicken breasts (with appropriate supplements to avoid nutritional deficiencies, had started to increase. This might possibly have been related to the MP, but could also have been something that would have occurred in any case. I found I needed to stop my usual foods for a longer period than usual (7-10 days) to bring the sensitivities down. Once I did that longer rotation one time, I was better, and my sensitivities are now beginning to come down slightly compared to pre MP levels (For more on the subject of allergies/sensitivities and the pulse test, see Issue 5 article).

Regular Phase Two and Phase Three

For those who choose the regular Phase Two, the usual rotation period is 10 days, because the antibiotic that is added stays in the body much longer. Caution must be used, because if the Herx becomes too strong, you have to endure it longer because it takes longer for the antibiotic to decrease. Very low doses are used to begin with (1/16 or 1/8 of a 250 mg tablet). Some people take longer to eliminate the antibiotic from the body, so may need to wait even longer than the recommended 10 day interval between doses before the Herx declines and it is time to take the next dose (see 3 day or longer dosing interval explanation). Otherwise, the antibiotic may accumulate to higher levels in the body. It is usual to avoid too intense an immune system reaction (Herx) to reduce the minocycline to 25 mg each time you increase the second antibiotic and then to gradually increase to the full 100 mg minocycline before increasing the second antibiotic to the next level. When beginning Phase Two, you should study all the information at the beginning of the Phase Two and Three Forum, not just the protocol guidelines. Changes are sometimes made to improve the protocol and so it is important to continually watch the web site for updates (

Phase Three involves combinations of 3 antibiotics. When starting a 3 antibiotic combination, the doses of all 3 should be lowered, generally to the starting doses for each, but it might lowered even more, if necessary. A recent change to the protocol involves somewhat lower maximum doses for some of the antibiotics when used in combinations of 3, so it is important to read about these new developments.

When one does the modified Phase Two first, one should then do the regular Phase Two for a while before going to Phase Three. Sometimes other two antibiotic combinations may be used before the regular Phase Two or Phase Three, as well. For patients who are particularly ill or sensitive, sometimes even lower initial doses than those mentioned already are used for the Phase Two and Three antibiotics. Longer periods between doses may be used (and occasionally someone finds a shorter interval is helpful).

As mentioned previously, it is important to study the various guidelines on the Marshall Protocol site thoroughly and it is usually very helpful to post progress reports regularly on the Marshall Protocol web site so that the volunteer staff can assist you in making adjustments when needed. By reporting your progress, you are also contributing to the research efforts of the Autoimmunity Research Foundation, since what you report on the site will be included in the ongoing Internet based study.

Editorial Note (2007): I have recently had some experiences with changes in my diet that has reinforced my belief that reducing my mostly “hidden” non IgE food sensitivities has been very important in my ability to do well on the Marshall Protocol. For more information, see: Carbohydrate, Chlorogenic Acid and Benicar Sensitivity.

Also, see:  Marshall Protocol Described in Laymen’s Terms: Transcript of a Presentation for a Lyme Support Group

For more Marshall Protocol Links, see:,,, and

Disclaimer: All articles provided on the SynergyHN website are for information only and are not intended as medical advice. An effort is made to be accurate, however readers are advised to verify what is presented here and check with their own doctors. No guarantee of accuracy is expressed or implied. Neither CISRA nor the author receives any funding or income from any organization or manufacturer connected with the topics discussed.

Written by synergyhn

October 28, 2008 at 11:48 pm

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