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Parasite Cleanse Protocol: Comprehensive Lab Testing, Therapeutic Diet, and Supplements

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Parasite Cleanse Protocol: Comprehensive Lab Testing, Therapeutic Diet, and Supplements

While the United States is considered a developed country with generally good public health infrastructure, parasitic infections are not wholly absent. While their prevalence is generally lower compared to developing regions of the world, they still pose a significant health problem in the U.S. Lack of clinician awareness and inaccurate testing contribute to the underdiagnosis of infections. (13

However, medical providers increasingly recognize the concept of "stealth" parasitic infections contributing to chronic diseases. This article will discuss the implications of parasitic infections on human health and a functional medicine approach to diagnosing and treating parasites.


What Are Parasites?

Parasites are organisms that live in or on another organism, known as the host, and derive nourishment from the host's body. They often harm the host in the process. Parasites can be found in various forms. In this article, we will focus on detecting and treating protozoa and helminths that infect the gastrointestinal tract.


Protozoa are microscopic, single-celled organisms that can multiply in humans. Protozoa are classified into four groups based on their movement mechanisms. Protozoa can be transmitted to humans through a fecal-oral route, causing a gastrointestinal infection, or through an arthropod vector, causing a blood infection. Some of the most common protozoan diseases include malaria, giardiasis, and cryptosporidiosis. (1, 14


Helminths are a group of multicellular parasitic worms categorized into three main groups: flatworms, thorny-headed worms, and roundworms. Most helminthic infections are transmitted by eggs in human feces, contaminating the soil in poor sanitation areas. The most common soil-transmitted helminthic infections are Ascaris, whipworm, and hookworm. (1, 14)

What Are the Effects of Parasites on Health?

Parasitic infections can lead to a range of health problems in humans and animals. They can cause diseases, weaken the host's immune system, reduce the host's reproductive success, and sometimes even lead to death. Parasites often cause gastrointestinal symptoms but can also cause a range of other health conditions, including chronic fatigue, weight loss, nutrient deficiencies and anemias, rashes and allergies, and autoimmunity. (6, 12

Signs & Symptoms of a Parasitic Infection

Signs and symptoms of a gastrointestinal parasitic infection include:

  • Nausea and vomiting
  • Diarrhea or constipation
  • Gas
  • Abdominal pain
  • Rectal itching
  • Visible worms, blood, and mucus in stool 
  • Fever
  • Fatigue
  • Muscle and joint pain

Parasite Infection Possible Causes 

Parasitic diseases can be transmitted to humans through a variety of mechanisms. The specific mode of transmission depends on the type of parasite and its life cycle. Here are some common ways in which parasitic diseases can be transmitted to humans:

Ingestion of Contaminated Food or Water

Many parasites, especially protozoa and helminths, can be transmitted by consuming contaminated food or water. This can occur when fecal matter containing parasite eggs or cysts contaminates food or water sources. Examples include Giardia, Cryptosporidium, and Entamoeba histolytica. (22

Vector-Borne Transmission 

Some parasites require a vector (usually an arthropod like a mosquito, tick, or fly) to transmit the infection from one host to another. The vector is an intermediary, transmitting the parasite while feeding on the host's blood. Diseases like malaria, dengue fever, and Chagas disease are transmitted through vector bites. (24

Direct Contact with Infected Animals

Parasitic infections can be transmitted through direct contact with infected animals or their contaminated environments. This can happen when humans handle infected animals, come into contact with their feces, or are exposed to areas where infected animals live. Toxoplasmosis is an example of an infection transmitted via direct contact with an infected cat. (21

Soil-Transmitted Infections

Some parasites, such as hookworms and Ascaris, release eggs into the soil through the feces of infected individuals. These eggs can then contaminate the soil and be picked up by people, often through skin contact with contaminated soil. (18

Sexual Contact

Certain parasites can be sexually transmitted from one person to another. Trichomoniasis is an example of a protozoal infection that can be transmitted through sexual activity.

Functional Medicine Lab Testing for Parasite Detection

A stool ova & parasite (O&P) test is the conventional test for diagnosing parasites in the digestive tract. Using an at-home test kit, you will collect a sample of your stool to send to the lab, which then uses a microscope to examine the sample to visualize parasites. False-negative results are common with this test, so multiple collections are generally recommended. (3

Stool Parasitology 

To increase testing accuracy, specialty stool tests combine microscopic and PCR diagnostic methods to evaluate stool samples. Similar to the O&P test, it is still recommended to collect multiple stool samples. Doctor's Data's parasitology test is one example that requires a three-day stool collection and screens for over thirty parasites, along with other markers associated with infection, such as fecal white blood cells.

Functional Medicine Labs to Help Individualize Treatment for Patients With Parasite Infections

Before starting a parasite treatment protocol, discerning factors responsible for setting up an internal environment hospitable to infection is important to improve treatment efficacy and prevent future infection recurrence.

Comprehensive Stool Analysis

A comprehensive stool analysis includes parasitology but also thoroughly evaluates gastrointestinal health and function to help identify factors, such as digestive enzyme insufficiency and microbial dysbiosis, that can make an individual more susceptible to gastrointestinal parasitic infections. 

Conventional Treatment for Parasite Infections

Conventional treatment for intestinal parasitic infections encompasses using a pharmaceutical antiparasitic drug. The drug choice and treatment duration will vary based on infection type, severity, and the patient's medical history. Common first-line antiparasitic medications include metronidazole, albendazole, and mebendazole. (9

A Functional Medicine Step-By-Step Parasite Cleanse Protocol

Healthy, non-pregnant patients are the best candidates for natural parasitic infection treatment. Natural cleanses require multiple agents dosed frequently and in high doses compared to their pharmaceutical counterparts, making them significantly more expensive. The agents also do have potential toxicity, and it is common to see mild adverse side effects during the protocol. 

Therapeutic Diet for Parasite Cleanse

Since intestinal parasitic infections are often associated with dysbiosis and increased inflammation, eating a whole-foods diet that limits inflammatory refined sugars, processed foods, and alcohol while emphasizing foods high in fiber, prebiotics, and probiotics is important. (10, 14

The most common food sources of parasites include undercooked or raw meats and seafood, raw fruits and vegetables (grown in contaminated soil), and unpasteurized milk. While following a parasite cleanse, it is important to wash and cook foods well and avoid common dietary sources of parasites to avoid reinfection. (5

Incorporating antiparasitic foods, such as garlic, pumpkin seeds, pomegranates, and papaya, can increase the efficacy of the natural treatment protocol. One study found that a mixture of honey and papaya seeds cleared the stools of parasites in over three-quarters of subjects. (7

Staying well-hydrated is another critical aspect of a parasite cleanse. Drinking adequate clean water daily prevents dehydration related to diarrhea and promotes healthy, daily bowel movements, promoting parasite excretion. (10, 14)

Supplements for Parasite Cleanse

Many natural supplements and combination formulas can be used for a parasite cleanse. Dosing in sufficient doses for adequate time is critical in ensuring a successful parasitic purge. 


Commonly known as wormwood, Artemisia absinthium is a broad-spectrum antiparasitic widely used to treat helminthic infections. Research supports its use in eradicating intestinal parasites and supporting healthy digestive functions, including stimulating the flow of gastric juices, bile, and blood in the digestive tract. (14, 15

Dose: 500 mg 2-3 times daily

Black Walnut

Black walnut, or Juglans nigra, is both a laxative and antiparasitic herb that is used to kill intestinal parasites and clear them from the digestive tract. (8, 11

Dose: 1-2 mL tincture three times daily


Allicin, the antimicrobial constituent of garlic, has demonstrated broad-spectrum antimicrobial activity against bacteria, fungi, and parasites. Research has shown its ability to successfully treat Giardia infections.

Dose: 450-900 mg three times daily

Detox Reactions During Parasite Cleanse

Parasites release toxins as they are killed, and the body may respond to this elevated toxin load with uncomfortable detox symptoms. This phenomenon is known as a Herxheimer, or die-off, reaction. For those who experience die-off, symptoms usually appear within 24-72 hours of starting an antiparasitic protocol and self-resolve within 3-7 days. Symptom severity varies and commonly seems flu-like in nature, with symptoms like fatigue, headache, body aches, increased gastrointestinal symptoms, and low-grade fever. Using natural supplements and complementary modalities to support detoxification pathways and reduce oxidative stress will help manage die-off symptoms. (4

Monitoring Progress in Parasite Cleanse

To catch and kill the parasite in all phases of its lifestyle, it is recommended to pulse-dose treatment. This looks like dosing supplements for two weeks on, then 1-2 weeks off, for three cycles. A parasite cleanse, therefore, generally requires 1-2 months for success. After the cleanse ends, stool parasitology testing should be repeated to confirm parasite eradication.

Learning More About Parasites



Parasitic infections may be more common than you think and can easily go undetected due to vague symptom presentation and inaccurate testing. If you suspect you may have an intestinal parasitic infection, speak with a functional medicine doctor to discuss testing and natural treatment protocols. A parasite cleanse should be undertaken under the eyes of a trained healthcare professional to minimize the risk of harmful side effects and drug-herb interactions.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

1. About Parasites. (2019). Centers for Disease Control and Prevention.

2. Allicin. ScienceDirect.

3. Brennan, D. (2021, June 5). What Is a Stool Ova and Parasite Test (O&P)? WebMD.

4. Cloyd, J. (2023, April 20). Treating a Herxheimer Reaction With Integrative Medicine. Rupa Health.

5. Common Food Sources of Parasites. Canadian Institute of Food Safety. Retrieved August 16, 2023, from

6. Greenan, S. (2021, December 1). How Undiagnosed Parasite Infections Cause Chronic Health Conditions. Rupa Health.

7. Intestinal parasites. Mount Sinai Health System.

8. Jha, B. K., Jung, H.-J., Seo, I., et al. (2015). Juglone induces cell death of Acanthamoeba through increased production of reactive oxygen species. Experimental Parasitology, 159, 100–106.

9. Kucik, C. J., Martin, G. L., & Sortor, B. V. (2004). Common Intestinal Parasites. American Family Physician, 69(5), 1161–1169.

10. Maholy, N. (2023, February 24). Integrative Medicine Treatment Protocol for Giardia. Rupa Health.

11. Marciano, M. Juglans nigra (black walnut). The Naturopathic Herbalist.

12. Parasitic Infection. (2023, April 7). Cleveland Clinic.

13. Parise, M. E., Hotez, P. J., & Slutsker, L. (2014). Neglected Parasitic Infections in the United States: Needs and Opportunities. The American Journal of Tropical Medicine and Hygiene, 90(5), 783–785.

14. Preston, J. (2023, January 31). Parasite Testing 101: A Complete Guide. Rupa Health.

15. Richards, L. (2023, February 16). What to know about wormwood.

16. Shelton, A. A. (2004). Sexually Transmitted Parasitic Diseases. Clinics in Colon and Rectal Surgery, 17(04), 231–234.

17. Soffar, S. A., & Mokhtar, G. M. (1991). Evaluation of the antiparasitic effect of aqueous garlic (Allium sativum) extract in hymenolepiasis nana and giardiasis. Journal of the Egyptian Society of Parasitology, 21(2), 497–502.

18. Soil-transmitted helminth infections. (2022, January 10). World Health Organization.

19. Soil-transmitted Helminths. (2019). Centers for Disease Control and Prevention.

20. Szopa, A., Pajor, J., Klin, P., et al. (2020). Artemisia absinthium L.—Importance in the History of Medicine, the Latest Advances in Phytochemistry and Therapeutical, Cosmetological and Culinary Uses. Plants, 9(9), 1063.

21. Toxoplasmosis: General FAQs. (2019). Centers for Disease Control and Prevention.

22. Transmission of Parasitic Diseases. (2019, February 26). Centers for Disease Control and Prevention.

23. Trichomoniasis. (2018). Mayo Clinic.

24. Vector-borne Diseases. (2020, March 2). World Health Organization.

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