This is a documentation page — an overview of what the Buhner Protocol is, what herbs it uses, and what each herb is understood to do. It is not a treatment guide, and it is not a recommendation. Describing a protocol does not mean endorsing it. Herbal treatment for Lyme disease is unvalidated by clinical trials and some herbs carry real risks. Anything here should be discussed with a qualified practitioner before acting on it.
Who is Stephen Harrod Buhner
Stephen Harrod Buhner (1952–2022) was an American master herbalist, author, and researcher. Over a career spanning more than thirty years, he wrote more than twenty books on herbal medicine, plant ecology, and the nature of healing systems. He lectured internationally and was widely regarded as one of the most scientifically rigorous thinkers in Western herbalism.
His interest in Lyme disease grew from extensive encounters with patients for whom conventional treatment had failed or was unavailable. What distinguished his approach from much of the herbal literature was an insistence on working from the underlying biology — understanding how Borrelia actually behaves in the body, what mechanisms it uses to evade immunity, and which plant compounds could plausibly interfere with those mechanisms. The result was a protocol grounded not in tradition alone, but in a synthesis of microbiology, immunology, and phytochemistry.
His foundational Lyme book, Healing Lyme, first published in 2005 and substantially revised in 2015, became the most referenced text in the herbal Lyme community worldwide. It was followed by two companion books dedicated to co-infections. The protocols described across these three volumes are what practitioners and patients collectively refer to as "the Buhner Protocol."
Five principles — in order of priority
Buhner's approach is not primarily about killing bacteria. This is the most important thing to understand about it — and the thing most often misunderstood. His five therapeutic priorities, listed in the order he considers most important, are:
Borrelia specifically targets collagen-rich tissues — joints, tendons, heart valves, the brain's blood vessel walls. Protecting and rebuilding these structures halts the physical damage the bacteria causes, regardless of whether the infection is active.
The goal is a regulated, functional immune response — not a stimulated one. Borrelia actively suppresses CD57 natural killer cells and dysregulates cytokine signalling. Restoring immune balance is considered more important than direct antimicrobial action.
Much of the suffering in Lyme disease is caused by the body's own inflammatory response — not the bacteria directly. Interrupting cytokine cascades reduces symptoms and prevents further tissue damage.
Joint pain, neurological symptoms, cardiac involvement, fatigue — each has targeted botanical support within the expanded protocol.
Direct antimicrobial action is the lowest priority in Buhner's framework. He argues that a functional immune system is ultimately what clears the infection, and that focusing primarily on "killing" without addressing the terrain is why many treatments — herbal and antibiotic alike — produce incomplete results.
This inversion of the usual medical logic — treat the host, not just the pathogen — is the conceptual foundation of the entire protocol.
What the research shows — and where it stops
In 2020, researchers at Johns Hopkins University published a study evaluating twelve herbs commonly used for Lyme disease. Seven of the twelve showed greater activity against Borrelia burgdorferi in laboratory conditions than standard antibiotics — including against the cyst (persister) forms that are notoriously resistant to doxycycline. The herbs included Cat's Claw, Cryptolepis, Chinese Skullcap, Japanese Knotweed, Sweet Wormwood, Thyme, and Oil of Oregano.
Seven of twelve tested herbal extracts showed greater in vitro activity against both motile and cyst forms of Borrelia burgdorferi than the antibiotics doxycycline and cefuroxime — including against persister forms that are resistant to standard antibiotic treatment.
This is significant — and it is also limited. In vitro activity in a lab does not automatically translate to clinical effectiveness in a living human body with different pharmacokinetics, absorption, metabolism, and immune context. No randomised controlled trials exist for the Buhner Protocol or any comparable herbal Lyme protocol. The absence of trial data does not mean the herbs don't work — it reflects the economic reality that herbs cannot be patented, and therefore attract little pharmaceutical research funding.
What exists is a substantial body of in vitro evidence, a large and growing community of patients and practitioners reporting clinical experience, and a mechanistic framework built on legitimate biochemistry and immunology. Taken together, this is more than most herbal approaches can claim — but it is also less than a clinically validated treatment protocol.
Buhner himself was consistently honest about this. He presented his work as a framework grounded in the best available science — not as proven therapy. That intellectual honesty is part of why his books remain influential.
Important cautions
Several herbs in the Buhner protocol have documented interactions with pharmaceutical medications. Japanese Knotweed and Chinese Skullcap can affect cytochrome P450 liver enzymes — the same pathway used to metabolise many prescription drugs, including antibiotics, anticoagulants, and cardiac medications. Anyone on prescription medication should discuss interactions with a qualified pharmacist or clinician before beginning any herbal protocol.
Die-off reactions — temporary worsening of symptoms as bacteria break apart — are common when beginning antimicrobial herbs. Buhner recommends starting all herbs at very low doses and increasing gradually over several weeks to minimise Herxheimer intensity. Adding Smilax and liver support from the beginning is specifically recommended for this reason.
Buhner estimated that most people should see meaningful progress within the first month of the core protocol. A full course — for those who respond — is typically 8 to 12 months. Severe or long-standing cases may require longer. This is a slow, systematic approach — not an acute treatment.
Buhner explicitly stated that his protocol can be used alongside antibiotic treatment and that doing so "will increase the positive outcomes from antibiotics considerably." The herbs are not presented as a replacement for antibiotic therapy — they are complementary, addressing the dimensions of the disease that antibiotics cannot reach.
The core protocol — three keystone herbs
The original core protocol consists of three herbs, selected for their combination of antimicrobial, anti-inflammatory, and immune-modulating properties. These three work synergistically and form the backbone of all subsequent additions.
Primary active compound: Resveratrol and related stilbenes, plus emodin and a range of polyphenols.
Why Buhner selected it: Japanese Knotweed root has the highest concentration of resveratrol of any plant. Resveratrol is a potent anti-inflammatory with documented activity across multiple cytokine pathways. Critically, it crosses the blood-brain barrier — making it one of the few botanicals with potential reach into the central nervous system, where Borrelia can establish persistent infection.
What it does in the protocol: Reduces neuroinflammation, modulates TNF-alpha and IL-6 cytokine signaling, protects collagen structures, and supports vascular integrity. Buhner considers it the single most important herb in the protocol for neuroborreliosis and Bartonella co-infection. Also active against Borrelia biofilms.
Typical form: Dried root powder or tincture. The root is the active part — not the stem or leaf.
Primary active compounds: Oxindole alkaloids, pentacyclic alkaloids, quinovic acid glycosides, and polyphenols.
Why Buhner selected it: Cat's Claw from the Peruvian rainforest has a long history of use for immune and joint conditions. Buhner's interest is specifically in its effect on CD57 natural killer cells — a subset of NK cells that are notably depleted in chronic Lyme patients. Restoring CD57 function is considered a marker of immunological recovery.
What it does in the protocol: Modulates the immune response without overstimulating it, reduces NF-kB inflammatory signaling, supports DNA repair, and provides direct anti-Borrelia activity. Also protects the gastrointestinal mucosa during treatment.
Important note on species: Buhner specifies Uncaria tomentosa — not Uncaria rhynchophylla (Chinese Cat's Claw / Gou Teng), which has different alkaloid content and is used separately for neurological presentations.
Important note on preparation: Only the TOA-free (tetracyclic oxindole alkaloid-free) form is recommended by Buhner, as TOA alkaloids may compete with the active pentacyclic alkaloids.
Primary active compound: Andrographolide and related labdane diterpenes.
Why Buhner selected it: Andrographis has documented antimicrobial activity against spirochetes. Buhner's rationale was based on its activity against Leptospira — a related spirochete — and its ability to penetrate the blood-brain barrier and reach neurological tissue. It is also a potent anti-inflammatory and NF-kB inhibitor.
What it does in the protocol: Direct antimicrobial pressure against Borrelia spirochetes, anti-inflammatory action in the CNS, and immune modulation. Reduces cytokine overactivation in neurological Lyme.
Critical caveat: A subset of people — estimated at 1–5% — develop significant allergic reactions to Andrographis, including hives, itching, and in rare cases systemic reactions. Because of this, Buhner updated the core protocol to list Andrographis as optional, with Siberian Ginseng as a safer alternative for those who cannot tolerate it. Anyone beginning Andrographis should start with very low doses and increase slowly.
These three herbs address the five priorities simultaneously: Japanese Knotweed for collagen and neuroinflammation, Cat's Claw for immune regulation, and Andrographis for direct antimicrobial and CNS anti-inflammatory action. No single herb does everything — the combination is the point.
The revised core — when Andrographis is not tolerated
Due to allergic reactions in some patients, Buhner introduced an updated version of the core protocol that can be used instead of or alongside the original:
Role in the updated core: Replaces some of Andrographis's immune-modulating function. Eleuthero is a classic adaptogen — it helps the body regulate stress hormones, supports adrenal function, and has documented immune-restorative properties. Buhner recommends it particularly for fatigue, depression, and decreased immunity — all common in chronic Lyme.
Important distinction: This is Eleutherococcus senticosus (Siberian Ginseng), not Panax ginseng, which has different properties and is not part of the protocol.
Role in the updated core: Astragalus is a deep immune tonic with documented effects on NK cell activity and T-cell function. However, Buhner is specific about timing: Astragalus is appropriate in early infection and as a preventative for people in Lyme-endemic areas — but it should not be used in active late-stage or chronic Lyme, where it may over-stimulate an already dysregulated immune response. This distinction is frequently misunderstood.
The expanded protocol — symptom-targeted additions
The expanded protocol consists of additional herbs selected for specific symptom presentations. These are not used by everyone — they are chosen based on an individual's pattern of symptoms. Most practitioners using the Buhner approach begin with the core herbs and add from the expanded list based on what the patient most needs.
One of the most important additions for neurological and psychiatric presentations. Baicalin, the primary active compound, is a potent anti-inflammatory that crosses the blood-brain barrier and reduces microglial activation — the brain's inflammatory immune response. Particularly useful for brain fog, anxiety, mood disturbance, and cognitive symptoms. Also has anti-Borrelia activity confirmed in the 2020 Johns Hopkins in vitro study.
Kudzu root contains puerarin and daidzein — isoflavones with documented vascular and neuroprotective properties. Buhner uses it to protect the cerebral vasculature from Borrelia-induced damage, improve blood flow to the brain, and support recovery from neurological Lyme. Often combined with Japanese Knotweed and Chinese Skullcap for neurological presentations.
Teasel Root has a long traditional use for musculoskeletal complaints and connective tissue repair. Buhner recommends it specifically for joint pain — particularly knee involvement — which is one of the hallmark presentations of Borrelia infection. In the Lyme community, Teasel Root has developed a strong following and some practitioners report it to be among the most effective herbs for articular symptoms. Scientific understanding of its mechanisms remains limited.
Stephania contains tetrandrine and related bisbenzylisoquinoline alkaloids with anti-inflammatory and calcium channel-modulating properties. Buhner recommends it for neurological complications (including Bell's palsy), cardiac involvement, and eye symptoms — specific manifestations of disseminated Lyme. It is not a first-line herb and is typically added when these specific presentations are present.
Buhner uses Smilax specifically for its ability to bind bacterial endotoxins in the gut — reducing the toxic load from Borrelia die-off. This makes it particularly relevant during Herxheimer reactions, where large amounts of bacterial debris enter the bloodstream. Also has anti-inflammatory and liver-supporting properties.
Silymarin, the active compound in Milk Thistle, is one of the most well-documented hepatoprotective agents in phytomedicine. Buhner includes it to protect the liver during prolonged herbal treatment — particularly when multiple herbs with significant hepatic processing are used simultaneously. A standard supportive addition for anyone on a longer protocol.
Buhner specifically recommends Ashwagandha for two common Lyme symptoms: sleep disturbance and cognitive difficulties (memory and concentration). Withanolides, the primary active compounds, are adaptogenic and neuroprotective — documented to reduce cortisol, support thyroid function, and improve sleep quality. One of the more accessible and widely used additions from the expanded protocol.
Used specifically for cardiac presentations — palpitations, arrhythmia, and Lyme carditis. Hawthorn berries and flowers contain procyanidins and flavonoids that have documented cardioprotective and antiarrhythmic properties. Added when cardiac symptoms are present, often alongside Stephania.
Co-infection-specific protocols
Buhner dedicated two full books to the treatment of Lyme co-infections. Each co-infection has its own herbal protocol, which is typically used alongside — not instead of — the core Lyme protocol. The following are the primary herbs Buhner recommends per pathogen.
A parasite that infects red blood cells — similar to malaria in its mechanism. Key symptoms: air hunger, drenching night sweats, cyclic fevers, chills, and palpitations. Does not respond to doxycycline; requires antiprotozoal treatment.
- Cryptolepis sanguinolenta — antiprotozoal, systemic antimicrobial; primary herb for Babesia according to Buhner's website
- Alchornea cordifolia — antiprotozoal, immune-modulating, West African traditional antimalarial
- Sida acuta — protects red blood cells from parasitic invasion; broad-spectrum antimicrobial
- Artemisia annua / Artemisinin — standardised extract; documented antiprotozoal activity related to its antimalarial properties
- L-arginine supplementation — Buhner notes Babesia is sensitive to L-arginine; supplementation supports nitric oxide pathways that inhibit the parasite
An intracellular bacterium that invades red blood cells and endothelial cells. Key symptoms: burning nerve pain, foot and shin pain, stretch-mark-like skin streaks, sudden rage or anxiety, and vascular symptoms. Standard Bartonella blood tests frequently miss tick-associated strains.
- Japanese Knotweed — already in core protocol; Buhner considers it the primary herb for Bartonella due to its vascular and anti-inflammatory activity
- Houttuynia cordata — Yu Xing Cao; broad-spectrum antimicrobial, particularly useful for intracellular pathogens; Chinese traditional medicine herb
- Sida acuta — protects red blood cells from Bartonella-mediated invasion; used in both Babesia and Bartonella protocols
- Cordyceps — medicinal fungus; cytokine modulation, immune support, particularly useful for fatigue associated with Bartonella
- Chinese Skullcap — for neurological and psychiatric Bartonella presentations
Bacteria that infect white blood cells, causing acute flu-like illness with fever, chills, muscle aches, and headache. Typically present in the early phase after a tick bite. Both respond to doxycycline but persistent symptoms after treatment are increasingly recognised.
- Ashwagandha — primary herb; supports immune recovery and reduces the fatigue and cognitive symptoms that dominate these infections
- Chinese Skullcap — anti-inflammatory, cytokine modulation; documented activity against related obligate intracellular organisms
- Andrographis — antimicrobial and anti-inflammatory; included where tolerated
- Cat's Claw — immune regulation; already in core protocol
Cell-wall-deficient bacteria that are inherently resistant to beta-lactam antibiotics. Associated with fatigue, neurological symptoms, and respiratory involvement. In the context of chronic Lyme, Mycoplasma is thought to amplify immune dysregulation and cognitive symptoms.
- Japanese Knotweed — core anti-inflammatory; also has activity against cell-wall deficient organisms
- Chinese Skullcap — neurological and systemic inflammation
- Cordyceps — immune modulation and fatigue
- Bidens pilosa — broad-spectrum antimicrobial; documented activity against Mycoplasma species
- Full protocol detailed in Buhner's book "Healing Lyme Disease Coinfections"
The source texts
The complete protocols described above come from three primary books. These are the authoritative sources — this page is a summary overview, not a substitute for the detail in the books themselves.
Second edition (2015). The foundational text. Contains the full core and expanded protocol for Borrelia, the philosophy of treatment, detailed herb monographs, and coverage of Chlamydia and Rocky Mountain Spotted Fever co-infections. The first edition (2005) is also widely referenced but the second edition significantly updates the herb science and protocol recommendations.
Published 2015. Covers the three co-infections that most often accompany Borrelia. Each pathogen is covered in depth — biology, clinical presentation, and full herbal protocol. The Babesia section is the most frequently referenced part of this book.
Published 2013. Dedicated to Bartonella and Mycoplasma — two co-infections that are particularly complex and poorly understood. Contains the full herbal protocols for both, along with detailed analysis of their mechanisms of pathology.
All herbs at a glance
A summary of the full protocol — all pathogens and their primary herbs in one place.
| Target | Primary herbs | Protocol type |
|---|---|---|
| Borrelia (Lyme) | Japanese Knotweed, Cat's Claw, Andrographis | Core |
| Neurological | Chinese Skullcap, Kudzu, Japanese Knotweed | Expanded |
| Joints | Teasel Root, Cat's Claw | Expanded |
| Cardiac | Hawthorn, Stephania | Expanded |
| Babesia | Cryptolepis, Alchornea, Sida acuta, Artemisinin | Co-infection |
| Bartonella | Japanese Knotweed, Houttuynia, Sida acuta, Cordyceps | Co-infection |
| Ehrlichia / Anaplasma | Ashwagandha, Chinese Skullcap, Andrographis | Co-infection |
| Mycoplasma | Japanese Knotweed, Chinese Skullcap, Bidens pilosa | Co-infection |
Back to the full overview of herbal, ILADS, and standard antibiotic approaches — a map before going deeper.
Return to the full step-by-step path through Lyme disease.
Healing mindset checkpoint
Reading about herbal protocols can be both hopeful and overwhelming. There is a lot here. You do not need to understand or act on all of it at once. Take the parts that are relevant to where you are right now.
Read about healing mindset →Sources and further reading
- Buhner S.H. — Healing Lyme (2nd ed., 2015), Healing Arts Press
- Buhner S.H. — Natural Treatments for Lyme Coinfections (2015), Healing Arts Press
- Buhner S.H. — Healing Lyme Disease Coinfections (2013), Healing Arts Press
- Feng J. et al. — Evaluation of natural and botanical medicines for activity against growing and non-growing forms of B. burgdorferi. Front Med (Lausanne). 2020;7:6
- Shor A., Schweig S. — Review of herbal medicines with anti-borrelial activity. Journal of Integrative and Complementary Medicine, 2023
- Ross M. — Best herbal antibiotics for Lyme, Bartonella, and Babesia. treatlyme.com (updated 2025)
Last updated: March 2026