Quick answer: This is the protocol I commonly recommend to my patients, personalized for each person. It runs about 120 days: start the elimination diet with gut-lining support, add anti-inflammatory and anti-microbial support, then microbiome support, then digestive enzyme and probiotic support, and finally reintroduce foods. Supplement choices and doses are set with your provider.
Key takeaways
This leaky gut protocol runs in phases over about four months and is personalized for each person.
It starts with an elimination diet and gut-lining support, then moves through inflammation and microbial balance, microbiome support and digestive support.
The final phase brings eliminated foods back one at a time with a food diary, so you can learn which foods sit well with you.
Quick answers
How long is the leaky gut protocol schedule?
About 120 days, split into phases, and it is personalized for each person.
What are the phases?
Elimination diet with gut-lining support, then inflammation and microbial balance support, then microbiome support, then digestive enzymes and probiotics, and finally food reintroduction.
When are foods reintroduced?
Near the end, around days 111 to 120, one food at a time with a food diary.
Should I follow this schedule on my own?
I recommend working with a provider, because supplements can interact with medications. A free 15-minute consult is a simple place to start.
Educational information only, not medical advice.
How the schedule works
Each individual is unique and may need changes, but these components usually stay the same. Supplement products and doses are personalized and discussed in a visit. Overview of the phases: the four-phase approach.
Days 1–30: Start the elimination diet
Remove potential trigger foods (see foods to avoid) and begin gut-lining support.
Days 31–50: Anti-inflammatory and anti-microbial support
Continue the elimination diet and gut-lining support, and add supplements that focus on inflammation and microbial balance.
Days 51–80: Microbiome support
Continue the diet and foundations; finish the anti-microbial phase; begin probiotic support, which may include Saccharomyces boulardii.
Days 81–110: Digestive support
Add digestive enzymes to help break down proteins, carbohydrates and fats, plus probiotic support.
Days 111–120: Finish and reintroduce
Finish supplements and begin reintroducing eliminated foods one at a time, using a food diary. See reintroducing foods.
Other supplements sometimes considered
Caprylic acid is sometimes considered, as are herbal formulas traditionally used for parasites (such as wormwood, black walnut, clove, goldenseal and garlic); these can interact with medications and are not for pregnancy. Betaine HCl is another option, only under professional guidance.
Why personalization matters
Supplements can interact with medications and conditions. Please don’t start this protocol without working with a provider.
Gut health and healthy aging
A structured, phased approach supports the gut lining, microbiome and digestion, the foundation for lower inflammation as you age.
When to see a naturopathic doctor
It may be time to see a naturopathic doctor if you have ongoing bloating, gas, diarrhea or constipation, or food reactions that seem to be multiplying. The same is true if you have fatigue, skin flares or joint aches alongside gut symptoms, or if you want a personalized gut plan instead of guessing.
See a medical provider promptly for blood in your stool, black stools, unexplained weight loss, persistent vomiting, severe abdominal pain, fever, or trouble swallowing.
What the research shows
No published trial has tested this exact 120-day schedule, so the research below covers individual pieces of it rather than the plan as a whole.
Gut-lining support often includes L-glutamine. In a 2019 randomized trial by Zhou and colleagues, 106 adults who developed diarrhea-predominant IBS and a leaky gut test result after a gut infection took 5 grams of glutamine three times a day or a placebo for eight weeks. Symptom scores dropped by at least 50 points in 79.6% of the glutamine group compared with 5.8% on placebo, and the lactulose-to-mannitol permeability test returned to normal in the glutamine group only. Side effects were low and similar in both groups. This was a single-center trial in a narrow group, so the authors called for larger studies before the results are applied broadly.
For the probiotic phase, a 2010 review and meta-analysis by McFarland looked at 27 randomized trials of Saccharomyces boulardii in 5,029 adults. In trials of people taking antibiotics, S. boulardii cut the risk of antibiotic-linked diarrhea roughly in half (risk ratio 0.47). Evidence for other gut conditions was described as promising but not yet strong enough. The review mixed many different conditions and doses, which limits how precisely the numbers apply to a gut protocol.
Herbal formulas need care. In a 2008 study by Gurley and colleagues, 16 healthy volunteers took goldenseal or kava for 14 days, then a test dose of the sedative midazolam. Goldenseal raised blood levels of midazolam by about 60% and lengthened its half-life from about 2 to 3.2 hours by blocking the CYP3A liver enzyme, while kava had no effect. The study was small and used one test drug, but it shows why herbs in a gut protocol should be checked against your medications.
Want help finding the root of your gut symptoms?
A free 15-minute consultation with Dr. Kneessi. No cost, no obligation. In-office or by telehealth.
Questions to bring to your clinician
These questions can help you get the most out of your next visit.
Which phase of this kind of gut protocol would make sense for me to start with?
How could the 120-day schedule fit around my work and family life?
Which parts of the schedule could be adjusted for my needs?
How would we check in on my progress along the way?
Frequently asked questions
How long is the Leaky Gut Protocol?
About 120 days, personalized for each person.
Can I do the protocol without a provider?
I recommend working with a provider, because supplements can interact with medications.
When do I reintroduce foods?
Near the end, around days 111–120.
Are herbal anti-microbials safe?
They can interact with medications and aren’t for pregnancy. Use with guidance.
Sources
- Zhou Q, Verne ML, Fields JZ, et al. Randomised placebo-controlled trial of dietary glutamine supplements for postinfectious irritable bowel syndrome. Gut 2019. PMID: 30108163. https://pubmed.ncbi.nlm.nih.gov/30108163/
- McFarland LV. Systematic review and meta-analysis of Saccharomyces boulardii in adult patients. World J Gastroenterol 2010. PMID: 20458757. https://pubmed.ncbi.nlm.nih.gov/20458757/
- Gurley BJ, Swain A, Hubbard MA, et al. Supplementation with goldenseal (Hydrastis canadensis), but not kava kava (Piper methysticum), inhibits human CYP3A activity in vivo. Clin Pharmacol Ther 2008. PMID: 17495878. https://pubmed.ncbi.nlm.nih.gov/17495878/
- Asher GN, Corbett AH, Hawke RL. Common Herbal Dietary Supplement-Drug Interactions. Am Fam Physician 2017. PMID: 28762712. https://pubmed.ncbi.nlm.nih.gov/28762712/
- NIH Office of Dietary Supplements: Probiotics
This article is for educational purposes only and is not medical advice. It does not replace an individual evaluation. Talk with your healthcare provider before starting supplements or changing medications, especially if you are pregnant, nursing, or managing a health condition.
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