When & How to Treat Parasites in Lyme Disease

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When & How to Kill Intestinal Parasites in Lyme disease Image from Marty Ross MD

Updated: 3/28/23

About Intestinal Parasites in Lyme Disease

Consider treating intestinal parasites in Lyme disease because they lead the immune system to produce too many cytokines. Cytokines create fatigue, body pain, poor thinking, and the whole range of symptoms seen in Lyme disease. Not only does Lyme trigger these cytokines, but other infections, as well, such as intestinal parasites can trigger cytokines. Read more about cytokines and steps you can take to lower them in Control Cytokines: A Guide to Fix Lyme Symptoms & The Immune System.

The problem with intestinal parasites is that they are difficult to diagnose. The way most doctors test for parasites is to perform a microscope stool exam. However, studies show that depending on the kind of parasite, testing can work anywhere from 20-90 percent of the time. This means that testing is very poor and not reliable—if the test result is negative.

Additionally, hidden parasites are a major cause of ongoing fatigue and dysfunction. In 1990, Leo Galland, MD showed that 50 percent of people with chronic fatigue syndrome had intestinal parasite infections that were missed by physicians.

When to Consider Intestinal Parasites in Lyme Disease

If You Have Symptoms

Consider treating intestinal parasites if you have ongoing intestinal symptoms, such as gassiness, bloating, intestinal cramping, and mushy/loose stools—even after treating for intestinal yeast overgrowth. Read more about diagnosing and treating yeast in these two articles: A Silent Problem. Do You Have Yeast? and Kills & Prevents Yeast: A Brief Guide.

If You Have Risks

Even if you do not have intestinal gassiness and bloating, consider treating intestinal parasites if you have traveled to less-developed countries where you could have gotten parasites from contaminated food or water. Also, consider parasites if you drink well water, even if the well has tested clean. If you are an outdoors person who drinks untreated water from rivers or lakes, consider treating parasites, too.

If a person has a lot of intestinal symptoms after treating intestinal yeast overgrowth, consider treating for intestinal parasites early, near the beginning of treatment. In others who have risk of parasite exposures like I explained above, consider treating for parasites at the six-to-nine-month point in treatment if a person is following all of the steps in The Ross Lyme Support Protocol and is not getting a lot better.

What About Testing for Intestinal Parasites in Lyme Disease

Even though testing is not perfect, consider sending three separate stool samples to the lab for an ova and parasite microscope test to see if parasites can be identified. If possible, use a high-quality intestinal parasite lab like Genova Diagnostics. Also consider having an enzyme immunoassay (EIA) test performed for common parasites. This type of test attaches a marker to parts of parasites, so they can be seen. EIA testing can find common parasites 90 percent or more of the time when they are present. Yet, such testing does not exist for all types of parasites.

The reason to test is to see if the type of parasite is known. If you know which parasite you have, then the treatment option is to use a prescription antiparasitic for that specific parasite.

How to Treat Intestinal Parasites in Lyme Disease

If you can identify which parasite you have, use the prescription medicine that is shown to work best for that specific parasite.

If you are unable to figure out which parasite you have, then treat using one of the prescription options below or with the natural medicine option. Note that based on my experience, I find the prescription options to work well about 85-90 percent of the time. The natural medicine options seem to work about 60 percent of the time.


In my experience, Alinia works best but is quite expensive. Alinia is a universal anti-parasite medication that should work against most parasites. For more information, see Alinia: When & Why in Lyme Disease Treatment.

  • Alinia 500 mg 1 pill 2 times a day for 3 weeks, or
  • Biltricide 600 mg 1 pill 3 times a day for 3 days, then 21 days after the first pill take 1 pill 3 times a day for 3 more days.

Natural Medicines

Black walnut is a natural medicine used in parasite regimens based on its traditional use for this purpose. However, limited to non-existent science shows it works. Also, artemisinin and oregano oil may help. Use one of the two options below for at least two months.

Option One

Take all three of these herbal medicines at the same time.

  • Black Walnut 250 mg to 500 mg 3 times daily.
  • Artemisinin 100 mg 2 pills 3 times a day.
  • Oregano Oil 500 mg 3 times a day.

Option Two

Use Biocidin liquid drops or capsules. Biocidin is an herbal mix that has a number of herbs in it that may treat parasites. Two of these are black walnut and oregano. In addition, some of the other agents appear helpful. For more information, see Biocidin: A Potent Antimicrobial & Biofilm Breaker.

  • Biocidin Liquid. Start at 2 drops on the tongue 3 times a day and increase every other day by 1 drop per dose until you reach 10 drops 3 times a day. If you develop a Herxheimer die-off reaction, do not increase until it passes. Take without food, meaning at least 30 minutes before food and more than 2 hours after food.
  • Biocidin Capsules. Start at 1 capsule 2 times a day and after 2 days increase to 1 capsule 3 times a day. Every 2 days, add 1 capsule until you reach 2 capsules 3 times a day. If you develop a Herxheimer die-off reaction, do not increase until it passes. Take without food, meaning at least 30 minutes before food and more than 2 hours after food.


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. Force M, Sparks WS, Ronzio RA. Inhibition of enteric parasites by emulsified oil of oregano in vivo. Phytother Res. 2000;14(3):213-4. doi:10.1002/(sici)1099-1573(200005)14:3<213::aid-ptr583>3.0.co;2-u (View)
  2. Galland L. Intestinal Parasites, Bacterial Dysbiosis and Leaky gut. Foundation for Integrated Medicine. http://mdheal.org/parasites.htm. Accessed August 13, 2018.
  3. Krishna S, Bustamante L, Haynes RK, Staines HM. Artemisinins: Their growing importance in medicine. Trends Pharmacol Sci. 2008;29(10):520–527. doi:10.1016/j.tips.2008.07.004 (View)
  4. McHardy IH, Wu M, Shimizu-Cohen R, Couturier MR, Humphries RM. Detection of intestinal protozoa in the clinical laboratory. J Clin Microbiol. 2014;52(3):712–20. doi:10.1128/JCM.02877-13 (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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