Parasite Cleansing Protocol: The Uninvited Guests

Parasites are the great unmentionable of modern medicine. In the developed world, the assumption is that parasitic infection is a tropical problem — something you contract on a backpacking trip through Southeast Asia, not something living quietly in the suburbs of Houston or Saigon or Sydney. This assumption is wrong. Studies consistently show that parasitic infection in developed countries is far more common than most clinicians recognize. Blastocystis hominis alone is found in 15-30% of stool samples in Western populations. Dientamoeba fragilis, Giardia, pinworms, and others persist silently in millions of people who have never left their home country.

The clinical challenge: parasites are masters of evasion. They suppress immune detection, modulate host inflammatory responses, cycle through dormant and active phases, and embed in mucosal tissue where standard stool testing may not reach them. A negative stool test does not mean absence of infection. It means absence of detection.

Functional medicine takes parasites seriously — not as exotic curiosities, but as significant drivers of chronic digestive complaints, immune dysregulation, nutrient malabsorption, skin conditions, fatigue, anxiety, and insomnia.

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Common Parasites in Clinical Practice

Protozoa (Single-Celled Organisms)

Blastocystis hominis — The most commonly detected intestinal parasite worldwide. Its pathogenicity has been debated for decades. Current evidence suggests that certain subtypes (ST7 in particular) are clearly pathogenic, while others may be commensal in some hosts. Symptoms: bloating, diarrhea, abdominal pain, urticaria (hives), IBS-like presentation. Blastocystis is associated with increased intestinal permeability and altered microbiome composition. It can persist for years if untreated.

Dientamoeba fragilis — A flagellate protozoan frequently co-occurring with pinworms (Enterobius vermicularis). May use pinworm eggs as a vector for transmission. Symptoms: intermittent diarrhea, abdominal pain, fatigue, failure to thrive in children. Often missed on standard O&P (ova and parasites) testing because it does not form cysts and degrades rapidly in stool samples. PCR testing is far more reliable.

Giardia lamblia (intestinalis/duodenalis) — A flagellated protozoan that colonizes the upper small intestine, adhering to the mucosal surface with a ventral sucking disc. Directly damages tight junction proteins, causing intestinal permeability. Impairs fat absorption (steatorrhea). Classic presentation: watery, foul-smelling diarrhea, bloating, sulfurous belching, nausea, weight loss. Can cause lactose intolerance that persists for months after eradication. Waterborne transmission — contaminated streams, wells, municipal water failures.

Entamoeba histolytica — The only truly invasive Entamoeba species. Can penetrate the intestinal wall and migrate to the liver, forming amoebic abscesses. Most infections are asymptomatic, but invasive disease causes bloody diarrhea (amoebic dysentery), fever, and hepatic complications. Must be distinguished from the non-pathogenic Entamoeba dispar by PCR or antigen testing — they are morphologically identical under microscopy.

Cryptosporidium — A protozoan that infects the epithelial cells lining the small intestine. Causes profuse watery diarrhea. Self-limited in immunocompetent individuals (5-14 days) but can be severe and chronic in immunocompromised patients. Resistant to chlorine disinfection — standard water treatment does not reliably kill it.

Helminths (Worms)

Pinworms (Enterobius vermicularis) — The most common helminth infection in developed countries, especially in children. Female pinworms migrate to the perianal area at night to lay eggs, causing intense itching. This nocturnal migration explains the classic symptom of perianal itching that worsens at night, disrupting sleep. Transmission: fecal-oral, highly contagious within households. Eggs can survive on surfaces (bedding, toys, toilet seats) for 2-3 weeks.

Roundworms (Ascaris lumbricoides) — The largest intestinal nematode (up to 35 cm). Larvae migrate through the lungs before returning to the intestine (pulmonary migration phase can cause cough, wheezing — Loeffler syndrome). Adult worms in the intestine cause malnutrition, abdominal pain, and can form obstructive masses in heavy infections.

Hookworms (Necator americanus, Ancylostoma duodenale) — Larvae penetrate the skin (usually bare feet on contaminated soil), migrate through the lungs, and establish in the small intestine where they feed on blood. Cause iron-deficiency anemia, protein malnutrition, and fatigue. Interestingly, hookworm infection downregulates Th2 immune responses and has been studied as a potential therapy for autoimmune conditions and allergies (helminthic therapy).

Tapeworms (Taenia, Diphyllobothrium) — Acquired from undercooked pork (T. solium), beef (T. saginata), or fish (D. latum). Often asymptomatic except for passage of segments (proglottids) in stool. Diphyllobothrium latum can cause B12 deficiency by competing for B12 absorption in the ileum.

Strongyloides stercoralis — Unique ability to autoinfect — larvae can re-enter the host through perianal skin or intestinal mucosa, maintaining the infection indefinitely without external re-exposure. Can persist for decades. In immunosuppressed patients (especially those receiving corticosteroids), Strongyloides can cause hyperinfection syndrome — a potentially fatal disseminated infection. Must be ruled out before starting immunosuppressive therapy.

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Testing

GI-MAP (Quantitative PCR) — Gold Standard

The GI-MAP uses DNA-based polymerase chain reaction to detect parasitic DNA in stool. Advantages over traditional microscopy:

• Sensitivity: PCR detects parasitic DNA even when organisms are not visible in the stool sample — catching dormant cysts, low-level infections, and organisms embedded in mucus or tissue.
• Specificity: Distinguishes between pathogenic and non-pathogenic species (e.g., Entamoeba histolytica vs. E. dispar).
• Quantification: Reports parasite load in scientific notation, allowing tracking of treatment response.
• Single sample: More reliable than a single O&P, though not infallible.

The GI-MAP tests for: Cryptosporidium, Entamoeba histolytica, Giardia lamblia, Blastocystis hominis, Dientamoeba fragilis, Endolimax nana, Cyclospora, Chilomastix mesnili, Pentatrichomonas hominis, plus helminth markers including Ascaris, Enterobius, Necator, Ancylostoma, Trichuris, Taenia, Strongyloides, and Schistosoma.

Ova and Parasites (O&P) x3

Traditional microscopy examining stool for eggs, larvae, cysts, and trophozoites. Three separate samples collected on different days increase sensitivity because parasite shedding is intermittent. Even with three collections, sensitivity for many organisms is only 50-70%. Relies heavily on the skill of the microscopist. Still useful for visual identification of helminths and their eggs but inferior to PCR for protozoa.

Comprehensive Stool Analysis (CSA)

Combines culture, microscopy, and biomarker analysis. Provides broader context including digestive function markers, inflammation markers, and microbiome assessment alongside parasite detection.

Scotch Tape Test (for Pinworms)

Apply transparent adhesive tape to the perianal area first thing in the morning (before bathing or bowel movement). Pinworm eggs adhere to the tape and are visible under microscopy. Simple, inexpensive, and specific for Enterobius. Perform on three consecutive mornings.

Blood Testing

• Eosinophil count — elevated eosinophils (above 500 cells/mcL) can indicate helminth infection (tissue-invasive parasites stimulate eosinophilic response). Protozoa typically do not elevate eosinophils.
• Total IgE — elevated in helminth infections as part of the Th2 immune response.
• Parasite-specific antibodies — available for Strongyloides, Toxoplasma, Echinococcus, and others. Useful for tissue-invasive parasites that may not be detected in stool.

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The Lunar Cycle Connection

Traditional herbalism — across cultures from Ayurveda to European folk medicine to traditional Chinese medicine — has long associated parasite treatment with the full moon. This is not superstition. There is biological rationale.

Parasites, particularly helminths, have reproductive cycles influenced by the host’s hormonal fluctuations. Melatonin and serotonin levels shift with the lunar cycle — melatonin drops during the full moon (due to increased ambient light), and serotonin rises. Since 95% of the body’s serotonin is produced in the gut, this shift affects intestinal motility and the gut environment. Some parasitologists have observed that parasites appear more active and reproductively engaged during the full moon phase, potentially making them more vulnerable to antimicrobial agents.

The traditional protocol: begin antiparasitic treatment 5 days before the full moon, continue through 5 days after — a 10-day window centered on the full moon. Repeat for 2-3 consecutive lunar cycles to catch organisms at different lifecycle stages.

Is this evidence-based in the Western randomized-controlled-trial sense? Not yet. But the clinical tradition is deep, the biological plausibility is real, and the approach — pulsed treatment aligned with reproductive cycles — is sound parasitological strategy regardless of whether the lunar mechanism is confirmed.

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Drainage Support — FIRST

This is the most critical and most frequently skipped step. Before killing parasites, you must ensure the body can eliminate the die-off debris. Dead parasites release endotoxins, ammonia, and metabolic waste. If drainage pathways are congested — if the bowels are sluggish, the liver is burdened, the lymphatics are stagnant — these toxins recirculate and the patient feels terrible. Severe die-off reactions (Herxheimer) are not inevitable. They are a sign of inadequate drainage preparation.

Bowel Drainage (Non-Negotiable)

The patient must be having 1-2 well-formed bowel movements daily before beginning any antimicrobial or antiparasitic protocol. Constipation during parasite killing is a recipe for severe die-off and toxin reabsorption.

• Magnesium citrate — 300-600mg at bedtime. Osmotically draws water into the colon, softening stool and promoting motility. Start low and titrate to bowel tolerance.
• PHGG (Partially Hydrolyzed Guar Gum) — 5-7g/day in water. A soluble prebiotic fiber that normalizes bowel function (helps both constipation and diarrhea). Well-tolerated even during SIBO treatment. Produces butyrate.
• Triphala — 1000-2000mg at bedtime. An Ayurvedic formula of three fruits (Amalaki, Bibhitaki, Haritaki) that gently promotes intestinal motility, supports bile flow, and has mild antimicrobial properties. Also a rasayana (rejuvenative) in the Ayurvedic tradition.
• Vitamin C — 1000-3000mg/day in divided doses. Draws water to the bowel at higher doses. Also a potent antioxidant that supports detoxification.

Liver and Bile Support

The liver processes toxins released by dying parasites. Bile carries toxins into the intestine for elimination. Sluggish bile flow means toxins recirculate through enterohepatic circulation.

• Milk thistle (Silymarin) — 200-400mg/day. Silymarin stabilizes hepatocyte cell membranes, upregulates glutathione production, and promotes bile flow. The most studied hepatoprotective herb.
• TUDCA (Tauroursodeoxycholic acid) — 250-500mg/day. A bile acid that improves bile flow (choleretic), protects hepatocytes from bile acid toxicity, and has been shown to reduce ER stress. Particularly useful for patients with sluggish bile, history of gallbladder removal, or elevated liver enzymes.
• Bitters — dandelion root, gentian, artichoke leaf. Taken 15-20 minutes before meals. Bitter taste receptors on the tongue trigger a vagal reflex that stimulates gastric acid, pancreatic enzymes, and bile release. Swedish Bitters or Urban Moonshine are widely available commercial formulas.
• Beet root — 1-2 tablespoons of beet root powder or raw beet juice daily. Contains betaine, which supports bile flow and methylation. The deep red color of beets comes from betalains, which have anti-inflammatory and antioxidant properties.

Lymphatic Support

The lymphatic system is the body’s sewer network. Unlike the circulatory system, it has no pump — lymph moves through muscular contraction, gravity, and external manipulation. Stagnant lymph means stagnant detoxification.

• Dry brushing — Using a natural bristle brush, stroke toward the heart in long sweeps before showering. Stimulates lymphatic flow and skin detoxification. 3-5 minutes daily.
• Rebounding — Gentle bouncing on a mini trampoline for 10-15 minutes. The up-and-down motion opens and closes lymphatic valves, pumping lymph through the system. NASA research found rebounding to be one of the most efficient exercises for lymphatic movement.
• Castor oil packs — Soak a flannel cloth in cold-pressed castor oil, place over the right abdomen (over the liver), cover with plastic wrap and a heating pad. Apply for 30-60 minutes. Castor oil contains ricinoleic acid, which promotes lymphatic drainage, reduces inflammation, and supports bile flow. Traditional naturopathic remedy backed by emerging research.
• Gentle movement — Walking, yoga, qigong. Muscular contraction drives lymphatic flow. Avoid intense exercise during active die-off.

Drainage preparation timeline: Begin drainage support 2-4 weeks before starting antiparasitic agents. Confirm daily bowel movements before proceeding.

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Pharmaceutical Protocols

Blastocystis hominis

• Metronidazole 750mg 3x/day for 10 days — the standard first-line. Approximately 60-70% effective. Side effects: metallic taste, nausea, disulfiram-like reaction with alcohol.
• Nitazoxanide (Alinia) 500mg 2x/day for 3 days — a broad-spectrum antiparasitic. Effective against many protozoa and some helminths. Generally well-tolerated.
• Triple therapy for resistant cases: Secnidazole 2g single dose + Diloxanide furoate 500mg 3x/day x 10 days + Trimethoprim-sulfamethoxazole (TMP-SMX) 160/800mg 2x/day x 7 days. Used in refractory cases.

Giardia

• Metronidazole 250mg 3x/day for 5-7 days — approximately 80-90% effective.
• Tinidazole 2g single dose — better tolerated than metronidazole, shorter course, comparable efficacy.
• Nitazoxanide 500mg 2x/day for 3 days — alternative, especially for metronidazole-resistant strains.

Entamoeba histolytica

• Metronidazole 750mg 3x/day for 10 days for tissue infection, followed by a luminal agent (Paromomycin 500mg 3x/day for 7 days or Iodoquinol 650mg 3x/day for 20 days) to clear cysts in the intestinal lumen.

Pinworms (Enterobius)

• Mebendazole 100mg single dose, repeat in 2 weeks — kills adult worms but not eggs. The repeat dose catches worms that hatched from surviving eggs after the first dose.
• Albendazole 400mg single dose, repeat in 2 weeks — alternative.
• Pyrantel pamoate — available over the counter. 11mg/kg single dose, repeat in 2 weeks.
• Critical: Treat all household members simultaneously. Wash all bedding in hot water. Pinworm eggs are highly contagious and survive on surfaces for weeks.

Roundworms, Hookworms, Whipworms

• Albendazole 400mg single dose (roundworm) or 400mg daily for 3 days (hookworm, whipworm).
• Mebendazole 100mg 2x/day for 3 days.
• Ivermectin 200mcg/kg single dose — for Strongyloides: 200mcg/kg daily for 2 days.

Tapeworms

• Praziquantel 5-10mg/kg single dose — drug of choice for most tapeworm species.
• Niclosamide 2g single dose — alternative.

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Herbal Antiparasitic Protocol

For patients who prefer a natural approach, who have mild-to-moderate infections, or as an adjunct to pharmaceutical treatment. Many of these herbs have been used for parasites across cultures for thousands of years.

Core Herbal Agents

Mimosa pudica seed — 2 capsules (1g) 2x/day on an empty stomach, 30 minutes before meals. The seeds form a sticky, gel-like matrix in the intestine that physically traps parasites, their eggs, and biofilm debris. Works as a mechanical gut scrubber rather than a chemical antimicrobial. This is the backbone of the CellCore/Microbe Formulas approach. The gel also binds toxins, acting as a gentle binder. Start with 1 capsule and increase over a week.

Black walnut hull (Juglans nigra) — 500mg 2-3x/day, or 20-30 drops of tincture (green hull extract) 3x/day. Contains juglone, a naphthoquinone with potent antiparasitic and antifungal activity. Effective against both protozoa and helminths. Traditional North American and European antiparasitic. The green (unripe) hull is most potent. Also has antimicrobial effects against bacteria and yeast.

Wormwood (Artemisia absinthium) — 200-400mg 2-3x/day. Contains artemisinin and sesquiterpene lactones that disrupt parasite energy metabolism. Effective against Giardia, Blastocystis, and helminths. Artemisinin (from the related species Artemisia annua) is the basis of the Nobel Prize-winning antimalarial drug — traditional medicine confirmed by modern science. Do not use during pregnancy. Limit continuous use to 4-6 weeks, then take a 2-week break.

Clove (Syzygium aromaticum) — 500mg 3x/day, or 3-5 drops of clove essential oil in a capsule with a carrier oil. Contains eugenol, which is uniquely effective against parasite eggs — a critical gap that wormwood and black walnut do not fully address. The traditional “Hulda Clark” parasite protocol uses the combination of black walnut + wormwood + clove specifically because each component targets a different lifecycle stage: black walnut kills adults, wormwood kills larvae and intermediate stages, clove kills eggs.

Vidanga (Embelia ribes) — 500mg 2-3x/day. A classical Ayurvedic antiparasitic (krimighna — “worm destroyer”). Contains embelin, a benzoquinone with documented activity against helminths and protozoa. Used in Ayurvedic medicine for over 2,000 years as a rasayana and antiparasitic.

Neem (Azadirachta indica) — 400-500mg 2x/day. Contains azadirachtin and nimbin, which disrupt parasite reproduction and feeding. Broad-spectrum: effective against protozoa, helminths, bacteria, fungi, and even some viruses. Bitter taste stimulates bile flow. Traditional Ayurvedic and Southeast Asian medicine. Also supports blood sugar regulation and skin health.

Holy Basil (Tulsi, Ocimum tenuiflorum) — 500mg 2-3x/day. Adaptogenic herb with antiparasitic, antimicrobial, and immunomodulatory properties. Contains eugenol (like clove), ursolic acid, and rosmarinic acid. Supports the immune system’s ability to fight parasites while reducing the stress response that immunosuppresses the host. In Ayurveda, tulsi is considered sattva-increasing — it clarifies the mind and strengthens the spirit.

Sample Herbal Protocol Schedule

Full moon cycle approach (recommended):

• Days 1-10 (centered on full moon): Full-dose antiparasitic herbs + mimosa pudica + binders
• Days 11-18 (waning moon): Rest from antiparasitic herbs. Continue drainage support, binders, and gut repair (L-glutamine, zinc carnosine).
• Days 19-28/29 (waxing moon): Resume lower-dose herbal support + immune support (vitamin C, zinc, colostrum).
• Repeat for 2-3 full lunar cycles minimum.

This pulsed approach prevents adaptation, allows the body to process die-off between rounds, and catches parasites at different reproductive stages.

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Die-Off Management and Binder Protocols

Dying parasites release ammonia, endotoxins, LPS, and metabolic waste. Additionally, many parasites harbor their own internal bacteria and even viruses — when the parasite dies, these are released into the gut. This is why parasite die-off can feel worse than bacterial or yeast die-off.

Symptoms of Parasite Die-Off

• Extreme fatigue, malaise
• Headaches, brain fog
• Muscle and joint aches
• Skin breakouts, rashes, hives
• Digestive disruption (diarrhea, cramping, nausea)
• Insomnia, vivid dreams, nightmares (parasites can affect neurotransmitter metabolism)
• Mood swings, anxiety, irritability
• Flu-like symptoms

Binder Protocol

Binders are non-absorbable substances that bind toxins in the gut lumen, preventing reabsorption. They are essential during parasite killing.

• Activated charcoal — 500mg-1g, 2x/day. Broad-spectrum binder. Take at least 2 hours away from all medications, supplements, and food (it binds everything indiscriminately).
• Bentonite clay — 1 tablespoon in water, 1-2x/day. Negatively charged clay particles bind positively charged toxins (ammonia, heavy metals, mycotoxins). Take away from other supplements.
• Chlorella — 1-3g/day. Binds heavy metals and toxins. Also a nutrient-dense green algae providing chlorophyll, B-vitamins, and amino acids.
• Zeolite (clinoptilolite) — binds ammonia (a major parasite byproduct), heavy metals, and mycotoxins within its cage-like crystalline structure.
• BioToxin Binder or GI Detox+ — combination products containing multiple binders (charcoal, clay, humic/fulvic acids) designed for comprehensive toxin binding.

Binder timing is critical: Take binders at least 30-60 minutes before meals and at least 2 hours away from medications and supplements. Many practitioners recommend taking binders at bedtime, when they will not interfere with daytime supplements. Adequate water intake with binders is essential to prevent constipation.

Additional Die-Off Support

• Molybdenum 500-1000mcg/day — essential cofactor for aldehyde oxidase, which converts acetaldehyde and other aldehyde toxins into less harmful acids for excretion
• NAC 600mg 2x/day — glutathione precursor; supports liver detoxification
• Epsom salt baths — 2 cups magnesium sulfate in warm bath for 20-30 minutes. Promotes sulfation pathway detoxification and relaxation
• Hydration — minimum 2-3 liters filtered water daily. Add electrolytes if diarrhea is present.

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Duration and Treatment Considerations

Minimum Duration

Most parasite protocols require longer treatment than bacterial or fungal protocols because of lifecycle considerations:

• Protozoa: 2-3 treatment cycles (6-10 weeks minimum). Protozoa cycle between active trophozoite and dormant cyst forms. Cysts are resistant to many antimicrobials. Pulsed treatment catches organisms as they emerge from cyst form.
• Helminths: 2-3 treatment rounds, typically spaced 2 weeks apart to catch newly hatched organisms from eggs that survived the initial round.
• Recommended minimum: 2-3 full moon cycles for herbal protocols (approximately 2-3 months). Pharmaceutical protocols are typically shorter but may need repeating.

Family and Household Treatment

Pinworms, Giardia, and Blastocystis are highly contagious within households. If one family member tests positive:

• Test all household members — especially children, who are often asymptomatic carriers.
• Treat simultaneously — staggered treatment leads to re-infection between family members.
• Hygiene measures: Wash all bedding and towels in hot water at the start of treatment. Clean bathroom surfaces. Emphasize hand hygiene, especially before meals and after using the toilet. Keep fingernails short (pinworm eggs collect under nails).
• Pets: Some parasites are zoonotic (transmissible between animals and humans). Discuss pet deworming with a veterinarian.

Retest Protocol

• Retest with GI-MAP (or equivalent PCR stool test) 4-6 weeks after completing treatment
• If positive: repeat treatment with a different antimicrobial approach (switch from herbal to pharmaceutical or vice versa, or use a different combination)
• Some organisms (especially Blastocystis and Dientamoeba) are notoriously resistant and may require 2-3 treatment rounds with different agents

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Post-Treatment Gut Restoration

Parasite infection damages the intestinal mucosa, disrupts the microbiome, depletes nutrients, and increases intestinal permeability. Killing the parasite is only half the work. Rebuilding the terrain is the other half.

• L-Glutamine 5-10g/day — repair intestinal lining
• Zinc carnosine 75mg 2x/day — tight junction repair, mucosal healing
• Probiotics — Saccharomyces boulardii (during and after treatment), multi-strain Lactobacillus and Bifidobacterium after treatment completion. Spore-based probiotics for deep ecosystem rebuilding.
• Iron and B12 — replete if depleted (common after hookworm, Diphyllobothrium, or Giardia infection)
• Vitamin A 5,000-10,000 IU/day — mucosal immunity
• Colostrum 5-10g/day — immunoglobulins and growth factors for barrier repair
• Prebiotic fiber — reintroduce gradually (PHGG, acacia fiber, cooked and cooled resistant starch) to rebuild commensal diversity

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The Deeper Teaching

In Vietnamese folk medicine, they speak of con giun, con san — the worms, the parasites — with a matter-of-factness that Western medicine has lost. Deworming was a regular practice, not an emergency. Children received antiparasitic herbs with the changing seasons. The body’s relationship with parasites was understood as ongoing, not one-and-done.

The Coyote sees parasites as teachers of boundaries. A parasite exploits what you leave unguarded. It feeds on what you do not digest. It thrives in the stagnation you tolerate. The protocol is not just biochemical warfare — it is an exercise in reclaiming your terrain.

Open the drainage pathways first. This is the wisdom of sequence — you do not demolish a building before clearing the exit routes. You do not kill organisms faster than the body can process their remains. Respect the order of operations.

Then kill with precision. Not with panic, not with carpet-bombing, but with targeted, pulsed, lifecycle-aware strategy. The herbs and pharmaceuticals are tools. The intelligence is in the timing.

Then rebuild. Seal the borders. Replenish the defenders. Restore the fire that should have kept the invaders out in the first place — the stomach acid, the bile, the motility, the immune surveillance, the microbial ecosystem that says: this territory is occupied.

The body knows how to maintain sovereignty. It has been doing it for millions of years. Your job is not to fight the parasites for the body. Your job is to restore the conditions under which the body fights for itself.