Kills Babesia: A Brief Guide

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Updated: 2/2/23

Babesia Treatment Key Steps

In my experience, recovering from Babesia, one of the Lyme disease co-infections, requires two key action steps:

  • boost the immune system; and
  • kill Babesia germs with herbal or prescription antibiotics and antimalarials.

One Additional Step - Remove Babesia-fibrin Nests

In addition to these key steps, some with chronic Babesiosis require enzymes to break up nests of Babesia and the blood-clotting protein called fibrin that can form in narrow and small blood vessels. These Babesia nests limit blood flow to tissues and may block antimicrobials and the immune system from killing these germs. Lumbrokinase, a group of enzymes that comes from earthworms, is very effective at breaking up fibrin. Other options include nattokinase or serapeptase, but these enzymes are much weaker than lumbrokinase.

What the Research Says

Limited research shows prescription antimalarials work for one strain called Babesia microti. Research supports the combination of atovaquone and azithromycin. There is also research support for the clindamycin and quinine combination. These studies support a 7-to-10-day course of treatment. This is one reason why many insurers refuse to pay for Babesia treatments longer than 10 days. More recent research shows tafenoquine, a newer anti-malaria medication approved in 2018 by the FDA, has good effects against Babesia microti in the lab and in a recent case report.

However, no studies about Babesia treatment in Lyme exist. In Lyme, the experience of most experienced LLMDs is that it can take four to five months of continuous antimicrobials for Babesia to resolve.

Newer research also suggests that Babesia microti can be easy to clear. But some with chronic Babesiosis may have a different type of Babesia infecting them. One of these strains is called Babesia odocoilei. Unfortunately, standard Babesia labs do not currently effectively detect this strain. Babesia odocoilei may produce a false positive Babesia duncani tests. So many people who have a positive Babesia duncani test may, in fact, have a Babesia odocoilei infection instead of a Babesia duncani infection.  Babesia odocoilei may require longer and more complicated treatments, including lumbrokinase to break up the fibrin nests.

In clinical practice, many different combinations of herbal and prescription antimalarials work to cure Babesia. I explain these various combinations below. With these treatments—including steps to boost the immune system and to decrease cytokine inflammation—it is possible to cure Babesia 90-95 percent of the time, in my experience. This means 5-10 percent of people may relapse or require treatments involving several of the different approaches below.

Step One - Boost the Immune System to Cure Babesia

It is critical for Babesia recovery to take steps that boost the immune system. Boost the immune system following the first 10 steps in The Ross Lyme Support Protocol. These steps may

  • correct sleep,
  • decrease inflammatory cytokines,
  • help the immune system adapt to stress,
  • correct hormone imbalances,
  • provide essential micronutrients, and
  • remove yeast overgrowth in the intestines, if present.

Step Two - Use Combination Antimalarials to Cure Babesia

Babesia is a blood parasite like the parasite that causes malaria. Therefore, treating Babesia requires combinations of antimicrobials that are also used to treat malaria. Generally, treatments require four to five months. This length of time is required due to immunosuppression caused by Lyme. Moreover, curing Babesia requires treating at least one month longer than the average length of time a red blood cell lives after it is made by the bone marrow in the center of bones. A red blood cell lives for around three months.

As I noted previously, no useful medical research exists to guide treatment decisions for Babesia in someone who has Lyme. What follows is based on my experience treating Babesia in Lyme disease.

In general, if a treatment is working, the symptoms of Babesia should start to improve in one to two months. If they do not start to improve, then change to a different regimen. Read more about Babesia symptoms in How to Diagnose Babesia.

Tier One Babesia Treatments in Lyme Disease

The following approaches work about 85 percent of the time based on my experience. Dosing is for adults. All the tier one approaches are prescription medicines. Atovaquone-based treatments are more established and often have better insurance coverage. Quinoline-based treatments that include the newer tafenoquine and older primaquine are quite effective, but I reserve these for when atovaquone-based treatments are not working or for when a person has Babesia relapse.

Atovaquone-Based Treatments

Atovaquone/Proguanil Combinations

Atovaquone/Proguanil (Malarone) 250 mg/100 mg. Start the atovaquone/proguanil at 2 pills 2 times a day for 3 days, and then decrease to 1 pill 2 times a day. Combine it with one of the following:

  • Azithromycin (Zithromax) 500 mg 1 time a day;
  • Clarithromycin (Biaxin) 500 mg 1 pill 2 times a day;
  • Doxycycline 100 mg 2 pills 2 times a day; or
  • Minocycline 100 mg 1 pill 2 times a day.

Atovaquone Combinations

Atovaquone (Mepron) 750 mg/5 ml 2 times a day. In one to two months, if night sweats or other Babesia symptoms are not improving, then increase the dose to 10 ml 2 times a day. Combine it with one of the following:

  • Azithromycin (Zithromax) 500 mg 1 time a day;
  • Clarithromycin (Biaxin) 500 mg 1 pill 2 times a day;
  • Doxycycline 100 mg 2 pills 2 times a day; or
  • Minocycline 100 mg 1 pill 2 times a day.

Be sure to take atovaquone with fat because this increases its absorption. Take enough fat so the medicine does not cause nausea or diarrhea. Sources of fat include nuts, nut butter, butter, oils (like coconut oil or flaxseed oil), yogurt, cheeses, and avocado.

Quinoline-Based Treatments

Effective quinoline medicines include tafenoquine and primaquine.

Before starting one of these treatments get a glucose-6-phosphate dehydrogenase (G6PD) blood test done. If you have low G6PD, do not take these medicines. With low G6PD, taking these medications could lead to breakage or hemolysis of your red blood cells and severe anemia.


Primaquine 26.3 mg 2 pills 1 time a day with hydroxychloroquine 200 mg 1 pill 2 times a day. If hydroxychloroquine gives side effects or this treatment is not effective, stop the hydroxychloroquine and start atovaquone 750 mg/5 ml 2 times a day.


Tafenoquine 150 mg (Krintafel) 2 pills 1 time a day every week. Combine it with one of the following:

  • Azithromycin (Zithromax) 500 mg 1 time a day;
  • Clarithromycin (Biaxin) 500 mg 1 pill 2 times a day;
  • Doxycycline 100 mg 2 pills 2 times a day; or
  • Minocycline 100 mg 1 pill 2 times a day.

In addition, if these combinations are not working, add

  • Atovaquone 750 mg/5 ml 2 times a day.

Tier Two Babesia Treatments in Lyme Disease

The following regimens work 75-80 percent of the time based on my experience. Dosing is for adults.

Herbal Antimicrobials


Cryptolepis is an herbal medicine originally used in Ghana to treat malaria. Cryptolepis is my “go to” herbal medicine treatment for Babesia. It supports Babesia removal about 75 percent of the time. Take it as 5 ml 3 times a day. In addition to using cryptolepis to treat active Babesia, use it as a preventive medication in a person who has a Babesia relapse. See the relapse section below.


Artemisinin 100 mg is an herbal medication. Start at 2 or 3 pills 2 times a day for 3 days on the medication, then take 11 days off. Continue this 14-day cycle. The goal is to reach 5 pills 3 times a day on the 3 days the medication is taken. I use artemisinin this way to overcome resistance. Be aware, the dose on the 3 days is quite strong. Often it causes a worsening of the Babesia symptoms beginning on the second day and sometimes lasting until six days later. If a person is very medicine sensitive, I start at 1 or 2 pills 3 times a day.

Artemisinin resistance can occur for two reasons. First, the liver learns to clean artemisinin out more quickly after a person is on it for a few days. The other mechanism could be like what happens in malaria. In malaria, partial resistance develops in the germ after a few days. In malaria, it is shown that artemisinin works best by pulsing on and off the drug like I recommend above.

It is possible to combine artemisinin with

  • cryptolepis,
  • atovaquone-based treatments,
  • quinoline-based treatments, or
  • Mefloquine (see below).

Cryptolepis/Sida Acuta/Alchornea (CSA Tincture)

Cryptolepis/Sida Acuta/Alchornea combines three antimalarial herbs that support Babesia removal. Take 5 ml 3 times a day. Use this if the Cryptolepis alone is not working well enough.

How to Build an Herbal Medicine-Only Treatment

For herbal medicine-only treatments, start with cryptolepis as 5 ml 3 times a day. If this is not helping Babesia symptoms by two months, then add artemesinin as I recommend above or change to the CSA tincture.

Prescription Antimicrobials

Mefloquine Combinations

Mefloquine (Lariam) 250 mg is a prescription medication. Start at 1 pill daily for 5 days, and then take as 1 pill every 5 days. It may cause nausea on the first five days. Mefloquine dissolves and is stored in fat. It takes 5 days or longer to saturate or to fill up the fat. Once the fat is saturated, taking a pill every 5 days keeps the fat saturated.

Combine it with one of the following:

  • Azithromycin (Zithromax) 500 mg 1 time a day;
  • Clarithromycin (Biaxin) 500 mg 1 pill 2 times a day;
  • Doxycycline 100 mg 2 pills 2 times a day; or
  • Minocycline 100 mg 1 pill 2 times a day.

This medication is the most affordable option. In the US, mefloquine is about $70 per month. However, it can have significant mental health side effects like depression, hallucinations, or even psychosis. I only use it if there are no other affordable options for my patients.


Artemether/Lumefantrine 20 mg/120 mg (Coartem) is a prescription medication. Take 4 pills 2 times a day for 3 days. On the first day, take the second dose 8 hours after the first dose. On the second and third day, take each dose 12 hours apart. The first dose of the day on all three days should be at the same time. Coartem can be repeated every two, three, or four weeks. I suggest starting every 2 weeks and increasing the time between each cycle as long as symptoms do not return on the off-medicine days.

Tier Three Babesia Treatment in Lyme Disease

I call this the “if all else fails” approach. Generally, it is effective about 75-85 percent of the time. Clindamycin/Plaquenil/Quinine work, but they have many side effects that make them hard to take.

Clindamycin and Hydroxychloroquine

Clindamycin 300 mg (Cleocin) and either hydroxychloroquine 200 mg (Plaquenil) or Quinine Sulfate 324 mg is an old-time combination that can treat Babesia. However, it is very hard to tolerate for most people due to side effects. Hydroxychloroquine is a quinine-like medication that is easier to tolerate than the quinine sulfate, though quinine sulfate may be more effective.

Side effects of clindamycin that make it hard to tolerate include nausea, diarrhea, abdominal pain, and allergic-type reactions. Quinine sulfate can cause ringing in the ears, but can also cause muffled hearing and other severe neurologic conditions. Generally, as a quinine-like medication, Plaquenil does not seem to cause these problems.

  • Option 1. Clindamycin 300 mg 2 pills 3 times a day and quinine sulfate 324 mg 2 pills 2 times a day. If muffled hearing or other neurologic symptoms other than ringing in the ears develop, then decrease the quinine sulfate to 1 pill 2 times a day.
  • Option 2. Clindamycin 300 mg 2 pills 3 times a day and Plaquenil 200 mg 1 pill 2 times a day.

Comment on Dapsone and Disulfiram

Dapsone and disulfiram are effective treatments for Lyme persisters. Both have some potential effect at killing Babesia. However, I find that these are not that effective at killing Babesia. I do not use these in my Babesia treatment regimens.

Step Three - Remove Babesia Nests

At one to two months into a Babesia treatment, if there is not significant improvement in Babesia symptoms supporting the immune system and using combination antimicrobials, add lumbrokinase to break apart Babesia-fibrin nests. I also attack the Babesia-fibrin nests in any person who has a Babesia relapse. In this situation, I add lumbrokinase as I restart Babesia antimicrobials.

  • Lumbrokinase 16-20 mg 1 pill 2 times a day. If there is not a significant Babesia Herxheimer reaction, consider increasing the lumbrokinase to 2 pills 2 times a day after 1 month. Lumbrokinase must be taken on an empty stomach. This means a person should stop all medicines, supplements, and food 1 hour before taking the lumbrokinase through 1 hour after taking lumbrokinase. It is OK to take the lumbrokinase with water.

Relapse Prevention

In my experience, it is possible to cure Babesia in Lyme disease 90-95 percent of the time. However, several people relapse or may not ever be able to stop medications. If a person recovers from Babesia, but then relapses after the germ is under control with one of the above regimens, then try a preventive regimen.

  • Option 1. Atovaquone/proguanil 250 mg/100 mg (Malarone) 1 pill daily.
  • Option 2. Cryptolepis 5 ml 3 times a day for 2 or 3 weeks of each 4 week period. Find the frequency that works best.
  • Option 3. Artemisinin 100 mg 2 or 3 pills 3 times a day for 3 days in a row of each 14 days. Repeat this cycle continuously.


The ideas and recommendations on this website and in this article are for informational purposes only. For more information about this, see the sitewide Terms & Conditions.


View Citations

  1. Buhner SH. Natural Treatments for Lyme Coinfections: Anaplasma, Babesia, and Ehrlichia. Healing Arts Press; 2015.
  2. Carvalho LJM, Tuvshintulga B, Nugraha AB, Sivakumar T, Yokoyama N. Activities of artesunate-based combinations and tafenoquine against Babesia bovis in vitro and Babesia microti in vivo. Parasit Vectors. 2020;13(1):362. Published 2020 Jul 20. doi:10.1186/s13071-020-04235-7 (View)
  3. Institute of Medicine Committee on the Economics of Antimalarial Drugs. Antimalarial drugs and drug resistance. In: Saving Lives, Buying Time: Economics of Malaria Drugs in an Age of Resistance. National Academies Press; 2004. View)
  4. Lindner H. Chronic Babesiosis Caused by Babesia Odocoilei: Pathophysiology, Diagnosis and Treatment. Lecture presented at the Annual International Lyme and Associated Diseases Scientific Conference; October 2021; Orlando.
  5. Marcos LA, Leung A, Kirkman L, Wormser GP. Use of tafenoquine to treat a patient with relapsing babesiosis with clinical and molecular evidence of resistance to azithromycin and atovaquone. IDCases. 2022;27:e01460. doi:10.1016/j.idcr.2022.e01460 (View)
  6. Mordue DG, Wormser GP. Could the drug tafenoquine revolutionize treatment of Babesia microti Infection? J Infect Dis. 2019;220(3):442-447. doi:10.1093/infdis/jiz119 (View)
  7. Scott JD, Sajid MS, Pascoe EL, Foley JE. Detection of Babesia odocoilei in humans with Babesiosis symptoms. Diagnostics (Basel). 2021;11(6):947. doi:10.3390/diagnostics11060947 (View
  8. Vannier E, Gewurz BE, Krause PJ. Human Babesiosis. Infect Dis Clin North Am. 2008;22(3):469-488,ix. doi:10.1016/j.idc.2008.03.010 (View)
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About The Author

Marty Ross, MD is a passionate Lyme disease educator and clinical expert. He helps Lyme sufferers and their physicians see what really works based on his review of the science and extensive real-world experience. Dr. Ross is licensed to practice medicine in Washington State (License: MD00033296) where he has treated thousands of Lyme disease patients in his Seattle practice.

Marty Ross, MD is a graduate of Indiana University School of Medicine and Georgetown University Family Medicine Residency. He is a member of the International Lyme and Associated Disease Society (ILADS), The Institute for Functional Medicine, and The American Academy of Anti-Aging Medicine (A4M).

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