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Lyme Disease Treatment Guidelines

The Ross Lyme Support Protocol

Questions or Comments? Participate in Conversations with Marty Ross MD.


About The Ross Lyme Support Protocol


“Try my self-help Lyme disease treatment guidelines to speed your recovery. My protocol includes the same time-proven successful approaches I use with thousands of my patients. Now you can use these cutting edge approaches to live fully.”  Marty Ross MD


Managing your care alone. The Ross Lyme Support Protocol provides the essential steps to manage your care.

Working with a prescription only medical provider. You will do better taking these additional steps to improve your care.

Already working with an integrative medicine physician. UseT he Ross Lyme Support Protocol to provide your doctor additional ideas to assist you.

Diagnosis, Tests, Symptoms, and Relapse Prevention.


Relapse Prevention.



The Ross Lyme Support Protocol


Here are Lyme disease treatment guidelines for anyone with chronic Lyme and associated diseases.The Ross Lyme Support Protocol includes essential treatment steps that you should address at the beginning and throughout a Lyme disease treatment. It is designed to:

  • boost the immune system,
  • speed recovery,
  • kill the infections, and
  • protect and repair from the harmful effects of the infections and the herbal or prescription antibiotics.

While the following Lyme disease treatment approach focuses on a limited number of areas, it corrects most of the problems like:

  • low energy,
  • pain,
  • insomnia,
  • brain, neurologic, and cognitive dysfunction, and
  • immune compromise and suppression.

Herxheimer Die-­off Reactions. When a person starts a Lyme disease treatment or changes herbal and prescription antibiotics it is common to have some worsening. See Herxheimer Die-off Reaction: Inflammation Run Amok for more information about this and the steps you can take to treat it.

Treatment Length and persistence. See Getting Healthy: Will I? When? How Do I? for more information about Lyme disease treatment length and persistence. Generally, we recommend you stay on each of the natural medicines recommended below for a minimum of 6 months to see if they are helping. Natural medicines do help speed recovery, but treating Lyme still takes time. Once you have marked improvement then you can likely stop many of these natural medicines except for probiotics, curcumin, ashwagandha, and a good multi­vitamin.

Part 1. Sleep

(Use either a natural medicine or prescription medicine. Do not mix natural medicines and prescription medicines together as a first treatment but you can do so later.)

Natural medicines:

(You can mix these two together or use in combination with the prescriptions medicines if needed.)

L-­Theanine 100mg 1 to 6 pills a night 1 hour before bed. Do not exceed 1200 mg a day if using for nerve pain or anxiety during the day too. Excessive amounts in the day are very sedating, AND/OR

Herbal Combinations. 1 to 4 pills 1 hour before bed. (Common herbs in sleep combination pills include valerian root, hops, yams, wild lettuce, l -theanine, and others.)

Prescription medicines:

Zolpidem (Ambien) 10 mg 1 pill 30 min before bed (Use if your primary problem is getting to sleep. It is short acting.) AND/OR

Clonazepam (Klonopin) 1 mg .5 to 2 pills 30 min to 1 hour before bed. (Use if your primary problem is staying asleep. If you have both a falling and staying asleep problem try Ambien first.)

Additional Options:

See Sleep 101: The Basics for more information about sleep hygiene and additional herbal and/or prescription options for a Lyme disease treatment.


Sleep is often disturbed in chronic Lyme disease. Lack of adequate sleep worsens pain, increases fatigue, and suppresses the immune system. It appears that in response to infection, the excess inflammatory cytokines produced by the immune system decrease the output of sleep inducing hormones to the sleep centers of the brain. A restorative amount of sleep is 7 to ­9 hours of sleep a night. Sleep in the few hours before midnight is most restorative.

Part 2. Diet

Eat a paleo based diet rich in organic foods, healthy fats, proteins, and vitamin rich vegetables. This type of diet is low in simple sugars which decreases the chances of developing intestinal yeast. It also promotes brain health and supports the energy factories found in every cell called mitochondria. Because it is low in sugar it also decreases inflammation. For more detailed information about the diet see The Best Brain, Inflammation, Pain, Energy & Detox Diet Ever.

Part 3. Cytokine Control

 Natural medicine:

Curcumin 500mg 1 pill 3 times a day,


AntiCytokine Combination (a product that contains curcuminresveratrolblack tea extract, and N-Acetyl Cysteine (NAC) 1-2 pills 3 times a day.

Prescription medicine:

(There are no effective and safe options.)


     Cytokines are inflammatory chemicals made by the immune system in chronic Lyme disease. Lowering them with curcumin, resveratrol, black tea extract, NAC and antioxidants found in a good multi­vitamin (Part 5.) will

  • correct many lyme symptoms,
  • boost the immune system, and
  • limit Herxheimer die-­off reactions.

     See Control Cytokines: A Guide to Fix Lyme Symptoms & The Immune System for more information and additional herbal medicine options to use in a Lyme disease treatment.

     On the one hand cytokines are good because they turn on the immune system. They perform a number of functions that include:

  • making antibodies work more effectively,
  • increasing active white blood cells to fight infections,
  • recruiting white blood cells to the location of an infection,
  • turning on white blood cells to fight infections, and
  • decreasing viral and bacterial replication.

     On the other hand in chronic Lyme disease the immune system makes too many cytokines which is bad. Too many cytokines:

  • suppress the immune system,
  • cause pain,
  • decrease hormone production from organs like the thyroid and the adrenal glands,
  • disturb sleep,
  • decrease brain function,
  • increase fatigue and tiredness,
  • waste muscles, cause depression, and
  • decrease the function of various organs throughout the body resulting in many other symptoms and medical problems.

     At the beginning of treatment or when antibiotics are changed the cytokines are made in even greater amounts causing a person to feel much worse. This is called a Herxheimer die­-off reaction.

Part 4. Adaptogen

Natural medicine:

Ashwagandha 400mg 1­ to 2 pills in am and 1 to 2 pills between 1 to ­2 pm. Taking late in the day may disturb sleep.


     An adaptogen is a substance that helps the body deal with the harmful medical and emotional stress of being ill. Adaptogens have been used for centuries in Ayurvedic and Chinese medicine with great observed benefit. Based on animal experiments ashwagandha improves energy, immune function, and adrenal and thyroid function. It likely has additional beneficial effects that have not been researched.

Part 5. Hormones

(Read the Rationale section below in this part to determine on your own if you have low hormones.)

A. Adrenal Insufficiency

(Start with the natural medicine or prescription medicine. Do not use both together in the first treatment, but you can do so later if the symptoms of low adrenals persist.)

Natural medicine:

Ashwagandha 400mg 1-­2 pills in am and 1-­2 pills between 1 to ­2 pm. Taking late in the day may disturb sleep.

Prescription medicine:

(We rarely use this because there is a very small risk of immune suppression using prescription hydrocortisone. However, the doses we recommend are the normal amounts the adrenal glands should make. On the other hand, ashwagandha is a supportive herb that does not suppress the immune system but helps the adrenals work better.)

Cortef 5 mg 1 to 2 pills in am and 1­ to 2 pills between 1­ to 2 pm. Taking late in the day may disturb sleep.

B. Low Thyroid

Natural medicines:

(Some recommend iodine but too much can make thyroid conditions worse. Rather than taking iodine use a good multivitamin recommended in Part 5 to provide the essential micronutrients the thyroid requires.)

Prescription medicine:

Dessicated Thyroid 1⁄2 grain or Armour Thyroid 1⁄2 grain 1 pill in the morning 30 min before anything else and on an empty stomach with water only. Increase every 3 to ­4 weeks by 1⁄2 grain if low thyroid symptoms persist.


     A person could have normal range testing for each of the hormones but still have clinically low hormones. Because of the unreliability of testing, treatment for low hormones should occur if there are clinical symptoms of low hormones as long as treatment does not increase hormone levels above the upper end of normal. Hormones provide many functions in the body. Proper levels improve energy and help the immune system to work more effectively in a Lyme disease treatment.

     Low hormones occur often in chronic Lyme disease. Inflammatory cytokines made by white blood cells to fight Lyme decrease the effective functioning of an area of the brain called the hypothalamus and pituitary. This part of the brain produces chemicals that induce sleep and that regulate hormonal systems. Normally this part of the brain releases messengers such as thyroid stimulating hormone (TSH), adrenocorticotropin hormone (ACTH), and follicle stimulating hormone (FSH) to stimulate the thyroid, adrenal glands, and sex hormone organs respectively. Because of the dysfunction caused by the cytokines, these regulatory messengers are released based on an incorrect interpretation by the brain of the hormone environment. Thus measurements of these messengers is an unreliable way to determine the hormone status. Another way to check hormone status is to measure the actual hormone levels like T4/T3 (thyroid), or cortisol/dhea (adrenals), or estrogen/progesterone/testosterone (sex hormones). These tests give a broad range of normal however. 


Adrenal Insufficiency: fatigue, recurrent infections, poor recovery from infections, low blood sugar with shakiness and irritability relieved by eating, low blood pressure and dizziness on standing, afternoon crashing, and sugar cravings.

Low thyroid: fatigue, achiness, low body temperatures averaging below 98.0 F, cold intolerance, weight gain, constipation, and changes in menstrual periods.

Part 6. Essential Micronutrients

Natural medicine:

Multivitamin. Use a vitamin that has numerous amino acids, antioxidants, minerals, and various vitamin Bs including b12 and folate. We prefer vitamin powders from Thorne and Integrative Therapeutics.


     To heal and feel better requires a multi­vitamin with an essential set of vitamins, minerals, amino acids, and antioxidants. A good multi­vitamin improves functioning of the immune system, muscles, brain and nerves, hormones, organs including the kidney and liver, detoxification, and decreases inflammation. It also protects the body from the toxic effect of prescriptive antibiotics.

Part 7. Yeast

(Read the Rationale section below in this part to determine on your own if you have a current intestinal yeast overgrowth problem requiring treatment.)

Prevention or Treatment

  1. For yeast overgrowth prevention use probiotics and antifungals in A & B.
  2. For current intestinal yeast overgrowth treatment use probiotics and antifungals in A & C.

A. Probiotics: Required for Yeast Prevention or Treatment

Natural medicine:

Probiotic. Use a product shown to repopulate the intestines in scientific studies. Take at least 10 billion live cultures 1 hour away from antibiotics. During an active yeast infection consider increasing to 20 billion cultures one time a day or divided in to two doses.

B. Antifungals for Prevention:

(Use either the natural medicine or prescription medicine. You do not need to use both together.)

Natural medicine:

Herbal Combinations. 2 pills 2 times a day. (Common herbs found individually or mixed together include: pau d’arco, caprilic acid, rosemary oil, thyme oil, garlic, and grapefruit seed extract.)

Prescription medicine:

Nystatin 500,000IU 2 pills 2 times a day.

C. Antifungals for Treatment:

(Do this if you have a yeast screening score of 140 or higher (see below). When you complete treatment, then start yeast prevention antifungals as above. Use the natural medicine or prescription medicine option but not both together.)

Natural medicine:

Herbal Combinations. 2 pills 2 times a day. (Common herbs found individually or mixed together include: pau d’arco, caprilic acid, rosemary oil, thyme oil, garlic, and grapefruit seed extract.) This will take 3­ to 4 months to get yeast overgrowth under control.

Prescription medicine:

(Use both of the following together.)

Nystatin 500,000IU 2 pills 2 times a day, and

Fluconazole (Diflucan) 200mg 1 time daily for 30 days. Use in combination with nystatin to prevent drug resistance. This combination will take 30 days to get yeast under control.

Additional Options:

Some have great difficulty getting rid of intestinal yeast overgrowth. See Kills Yeast: A Brief Guide for more herbal and prescription medicine options.


      Too many yeast in the intestines (yeast overgrowth) is a common problem that occurs in those with chronic Lyme disease either during or prior to beginning Lyme disease treatment. Antibiotics used to treat Lyme can lead to too many yeast. Immune suppression prior to starting antibiotics can also cause yeast overgrowth. Yeast overgrowth can result in an ongoing systemic allergic reaction to the yeast that can suppress the immune system. Yeast overgrowth also leads to inflammatory cytokine excess that cause many of the Lyme disease symptoms and pain. Food allergies and sensitivities can be the result of yeast overgrowth too.

     There is not a useful diagnostic blood test or stool test for yeast overgrowth. While some may test for antibodies in the blood to intestinal yeast, antibodies are common even when yeast are in balance. In addition it is normal to have stool cultures grow yeast; so a culture does not indicate if yeast are in excess. For this reason, yeast are diagnosed using our yeast screening questionnaire. This questionnaire evaluates for the possibility of yeast overgrowth based on yeast overgrowth risk factors and intensity of symptoms. In general we find people benefit from treatment if the score is 140 or higher.

     At the beginning of a Lyme disease treatment, often before antibiotics are started it is essential to treat yeast. Doing so can limit the severity of Herxheimer die­-off reactions from treating Lyme because removing yeast removes one source of inflammatory cytokine excess.

        Questions or Comments? Participate in Conversations with Marty Ross MD.

Part 8. Lyme Infection Treatment

(Take either the natural medicines or the prescription medicines. Do not take both together at the beginning, although you can do so later.)

A. The First Month

Natural medicines:

Otoba Bark Extract and Cat’s Claw5 drops 2 times a day of each herb and increase the dosing every 2 days by 1 drop per dose till taking 30 drops 2 times a day. Take on an empty stomach. Do not take 30 minutes before through 2 hours after having food, medicines, or supplements. If you get a Herxheimer die-­off reaction do not advance the dose till it decreases.

Prescription medicines:

(We generally start with oral antibiotics. For considerations about IV antibiotics see A Lyme Disease Antibiotic Guide.)

Doxycycline 100 mg 2pills 2 times a day or 4 pills 1 time a day. Take with food to prevent nausea. Do not take with calcium supplements or calcium fortified dairy products like milk or cheese or milk substitutes like rice milk.


Clarithromycin (Biaxin) 500mg 1 pill 2 times a day.

B. After the First Month

If you are on otoba bark extract and cats claw remain on 30 drops 2 times a day.

If you are on prescription medicines see A Lyme Disease Antibiotic Guide. You will need to work with your physician to add an additional antibiotic(s) to treat all 3 forms of the lyme germ.


     Lyme exist in three different forms. These are the spirochete, the l­-form (lives in cells), and the microscopic cyst form. A Lyme disease treatment should treat all three forms at the same time. However at the first treatment take care to avoid an intense die-­off reaction by starting one prescription antibiotic only.

     Otoba bark extract and cat’s claw treat all three forms of the germ. Because these herbs are dosed using drops, they can be more easily regulated to manage a die-off reaction by not increasing the dose until the reaction lessens if present. In our experience any oral antibiotic combination works as well as the otoba bark extract and cat’s claw combination which is 85% to 90% of the time.

     Doxycycline or Clarithromycin treat the spirochete and the l-­form, after the first month if a Herxheimer die-­off reaction is not too bad, an anti­cyst agent should be added. This is not done at the first visit because the Herxheimer die-­off reaction could be too intense.

Part 9. Detoxification

Reduce the total load of negative environmental influences on your health:

  • eat organic foods,
  • avoid gluten, scents, alcohol and tobacco, and
  • decrease emotional stress.

Vitamins: Support Liver detoxification by taking the multivitamin recommended in Part 5.

Diet: Drink water regularly to support kidney detoxification. A general rule of thumb is to drink 1/2 of your ideal body weight (measured in pounds) as ounces of non-caffeinated liquids a day. For example a person with a 150 pound ideal body weight should drink 75 ounces a day of non-caffeinated liquid. Eat healthy vegetables and a limited number of fruits a day for vitamins and for fiber. Fiber binds toxins in the intestines and promotes their removal from the body through regular bowel movements.

See Lyme Detoxification 101: The Basics for more detailed information.

Part 10. Coinfection Treatments for Bartonella and/or Babesia

If you have one of them do not start treatments for the co­infections at the initial visit. Wait one month or longer to adjust to the Herxheimer die­-off reaction from treating the Lyme infection and to stabilize on the supportive supplements.

If you have both of these co­infections you should treat one first before adding a treatment for the other. See Kills Bartonella: A Brief Guide and/or Kills Babesia: A Brief Guide for natural and prescription antibiotic approaches you can take to treat these infections.

Part 11. Additional Natural Medicines

Many other natural medicines to manage symptoms and problems exist. Wait one month after beginning a Lyme disease treatment to start these. Search The Treat Lyme Book to find recommendations for your specific problem or symptom.

Part 12. Exercise

This improves blood flow to all tissues and releases various chemicals that produce healing effects. If exercise makes a person worse, it should be done only to a tolerable level. Usually at the beginning of Lyme disease treatment exercise at any level should not be done due to tolerance issues. Overexercise which makes a person feel worse may suppress the immune system and impair healing.

Part 13. Special Considerations for Six Months and Beyond

There are additional steps you should consider by 6 to 9 months of Lyme disease treatment if you are not having adequate improvement. Consider adding:

Part 14. Health Decline after Doing Better

It is common to have ups and downs during the course of a Lyme disease treatment. In some cases there can be a significant decline after a person is doing better. In these cases consider yeast overgrowth of the intestines or relapse of a bartonella or babesia co­infection. In our experience the majority of major health declines are do to yeast overgrowth in the intestines. This is true even if significant symptoms of yeast do not exist. Excessive yeast in the intestines lead to increased levels of cytokines. Because excess cytokines cause many of the chronic Lyme disease symptoms, it could seem like your Lyme disease is getting worse. Yeast could be the cause of your decline if you have a number of these symptoms: increased sugar cravings, intestinal gassiness or bloating, recent vaginal yeast infection, oral yeast, and/or vaginal or rectal itching. For Information on diagnosing yeast see A Silent Problem: Do You Have Yeast? For yeast treatment information see Kills Yeast: A Brief Guide.