Digestive Health

The Best Treatment for Crohn’s Disease

By Kim Crawford, M.D. Last updated: May 2, 2022

Introduction to Crohn’s and Ulcerative Colitis-blog updated on 3/18/2021 and found here.

Inflammatory bowel disease (IBD) results from two disorders of chronic intestinal inflammation which affects approximately three million people worldwide: Crohn’s disease and Ulcerative colitis. There is no “fun” autoimmune disease, but IBD has its own special sort of misery that only those with the disorder can attest. While many treatments are quite similar, today’s discussion will focus on functional Crohn’s disease treatment.

leptinCurrently, allopathic (versus functional medicine) treatment for Crohn’s disease begins with corticosteroids and 5-aminosalicylic acid products, adds “immunomodulators” (Azathioprine, 6-mercaptopurine, methotrexate), and eventually, “biological agents” which are “TNF-alpha inhibitors” (infliximab, adalimumab, certolizumab, and golimumab).

Not one of these drugs are curative, and their long-term use often causes severe side effects including cancer. In fact, patient surveys show that almost 40% of Crohn’s patients use alternative therapies to complement their conventional medical care.

First, I’ll explain what causes Crohn’s disease. Then, I’ll review the following list of items that will help you get into and remain in remission:

  1. Change diet and carefully consume pharmaceuticals.
  2. Heal gut lining.
  3. Eat prebiotic foods and choose probiotic supplements.
  4. Take products to clear up toxic bacteria and/or yeast.
  5. Clear up toxins (if needed).
  6. Manage stress (cortisol).
  7. Balance hormones.
  8. Re-balance gut motility (often needed).
  9. Consider supplementation.
  10. Consider LDN.

The Root Cause of Crohn’s Disease

Conventional medicine teaches us that risk factors officially implicated with Crohn’s disease include smoking, low fiber-high carbohydrate diets, altered microbiomes and medications such as non-steroidal anti-inflammatory drugs. Each of these things will cause leaky gut; my findings will not contradict these conventions. Leaky gut is the root cause of autoimmune disease; including Crohn’s disease. Here are the principal causes of leaky gut.


The food you eat can cause leaky gut. People who consume the “standard American diet” (SAD) with it’s high-sugar, and high-processed foods content put their guts at risk. Also, GMO foods are now dominating the soy, wheat, and corn markets. Increasingly, GMO-gluten used ubiquitously in our food supply is being blamed for non-celiac gluten sensitivity and leaky gut. It’s estimated 25-75% of Americans have some type of food sensitivity. The most significant culprits are (in this order) wheat, dairy, eggs, and corn.

Consuming GMO foods (I have seen enough proof), artificial sweeteners, dyes, additives which don’t even sound like food as well as the massive amount of sugar (including HFCS and other hidden sugars) in our typical diet results in leaky gut. Add in non-sprouted grains and lectins (found mainly in beans which are un-soaked), caffeine, soda, fruit juice and alcohol, and it’s a wonder we all don’t have leaky guts. Maybe we all do to a certain degree; it’s hard to say. And we’ve only covered food and beverages thus far!

Chronic Stress

If you’re always stressed out, you have chronically elevated levels of cortisol. High cortisol alone can cause the breakdown of your GI lining. It does this by slowing down both peristalsis (GI motility) and digestion. Blood flow then decreases to all of the digestive organs which causes a higher concentration of toxic metabolites to then whittle away at your gut lining.



Painkillers are likely the most commonly used gut irritants that exist. Your gut lining can be interrupted by everything from Aleve and Ibuprofen to Vioxx or Tylenol. I’d be willing to bet that most people who take OTC pain relievers daily have some degree of leaky gut.

Another problematic category is antibiotics. Antibiotics upset the good:bad ratio of bacteria in the GI microbiome. Further, we have proton pump inhibitors which were never designed for more than short-term use. Many people use these PPI’s (Prevacid, Protonix, Nexium) for chronic heartburn and slowly nuke the lining of their GI tract.

Non-bioidentical hormone medications such as steroids (prednisone, Medrol) or birth control pills can help propagate the growth of excess candida (yeast), which can also damage the gut lining.

Hormonal imbalances can also cause chronic constipation such as low progesterone levels and low thyroid hormone levels. Indeed, this can readily lead to small intestinal bowel overgrowth (SIBO) as can many types of cancer chemotherapy agents. SIBO disrupts the gastrointestinal balance dysbiosis), often causing gas, bloating and eventually, leaky gut.

Gut Dysbiosis

Dysbiosis of the gut means that your GI microbiome (bacterial environment) is out of balance. A balanced GI microbiome is crucial for optimal GI function, immune function, and even (believe it or not) brain function. As you read previously, organisms such as yeast (candida) can invade the lining of the intestinal wall as can toxic E. Coli; a common culprit in SIBO occurrences. Other organisms such as giardia (a parasite) and Helicobacter pylori (responsible for ulcers and some cases of severe heartburn) can chip away at the intestinal lining leading to gastrointestinal symptoms and leaky gut. Toxins also contribute to leaky gut.

Environmental contaminants and toxins

Direct GI toxins we absorb or consume such as the fluoride in water, methylmercury in fish, or polluted air and water can damage our gut. A newly discovered direct GI toxin is the dust mite. Dust mites grow when there is a high degree of indoor mold; so this is yet another reason to make sure you have a mold-free home. Finally, there is a cumulative dose of toxins from food additives to un-filtered shower contaminants and even products we apply to our skin.

Now that you understand the causes, let’s begin the discussion of Crohn’s disease treatment in the Functional Medicine world.

Treat Underlying Gut Issues as an Integral Part of your Crohn’s Disease Treatment

Change your Diet

It’s necessary to eliminate foods that can cause leaky gut from your diet. At first, this is a huge modification that will ensure you don’t miss any offending foods. Quite often, after people develop a leaky gut, they develop a host of IGG-mediated food sensitivities which can cause a plethora of symptoms; I feel that it is better to start with a basic diet and then reintroduce certain foods when you have your symptoms under control.

If you are eating the standard American diet, quite a few modifications to what you normally eat will be necessary to reach remission. The first thing is to clean out your pantry and make a list of “allowed foods.” If you decide to follow a nutritional ketosis diet, here is the list. If you choose to follow my anti-inflammatory diet, we need to modify it slightly.

The easiest diet to follow is a strict GAPS plus AIP (auto-immune protocol) diet which restricts the “usual offenders” such as gluten, dairy, eggs, corn, processed foods, sugar, citrus, nightshade vegetables, grains, and legumes as well as caffeine and alcohol. It also restricts high FODMAP foods and is an “elemental diet plan.” I have combined the working diets in this one blog called; aptly, the best autoimmune diet. You cannot blame GI symptoms on any foods or spices if you eat this way for the two months it takes to heal a leaky gut. This diet is restrictive, but in two months, you can reintroduce some food items.

The Crohn’s Diet Plan

What Do You Eliminate?

  • Grains.
  • Legumes, such as beans, lentils, and peanuts.
  • Processed foods.
  • Seed oils, such as vegetable and canola oil.
  • Dairy products.
  • Refined sugars.
  • Eggs.
  • Nuts and seeds.
  • Herbs from seeds, like coriander, cumin, and nutmeg.
  • Coffee.
  • Chocolate.
  • Dried fruits.
  • Food additives, like gums and emulsifiers.
  • Nightshade vegetables, such as eggplant, potatoes, tomatoes, peppers, and okra.
  • Spices made from nightshades, like chili powder, paprika, cayenne, chipotle, red pepper.
  • Alternative sweeteners such as xylitol and mannitol with stevia being OK in tiny amounts.
  • Alcohol.
  • NSAIDs (Not food, but seriously bad for your gut lining.)

After eliminating all potentially allergenic foods, the remaining basics are:

  • Meat, fish, and poultry.
  • Low-sugar; small quantity fruits (berries only at first) and all vegetables, except for the nightshades.
  • Fruit oils (avocado, olive, coconut, palm) and animal fats such as ghee.
  • Bone broth (or gelatin/collagen).
  • Tea-Herbal is best, but some mildly caffeinated brands (loose, organic; not teabag) might be fine.
  • Vinegar: Restrict to apple cider initially.

Follow this practice until the “explosive diarrhea” wanes; for most people, this occurs within 3-4 weeks. At that time, you can add in a small cup of brewed coffee with a splash of additive free coconut milk. Coconut milk is not included at first because it is a high FODMAP food (believe it or not!) in more than very small quantities. Reintroducing food is usually quite personalized, so I can’t advise what to add from this list. Priority is also healing the mucous-lining of your GI tract which has holes in it (literally) while you are symptomatic.

Heal your Gut

Crohn’s disease starts with a leaky gut. Changing your diet is the first step in healing your gut. Using proper supplements for leaky gut is also essential; this includes a morning “leaky gut drink,” which includes collagen powder, “GI Rejuv” (containing all the right herbals), and antioxidants. Vitamin D levels need to be normalized, and probiotics should be added when the symptoms start to subside so that they don’t “leak back” into the bloodstream. You can start with prebiotic fibers in your diet, though. The next step is called re-balancing your microbiome.

Re-Balance your Microbiome

By definition, you have more “bad bacteria” than “good bacteria” lining your gut; or at the very least, not enough “good bacteria.” Use prebiotic fiber to feed the good bacteria and a little bit of “good yeast” to re-create a healthy gut microbiome. Start with asparagus, Jerusalem artichokes and naturally fermented (not pickled) foods such as sauerkraut. When symptoms subside, add probiotics. Do not make your own yogurt; you can’t have dairy, remember? You want 50 to 100 billion probiotic CFU’s per day. A mixture (in your main probiotic) of Lactobacillus species and Bifidobacterium species is necessary. A generic product, VSL3, has yielded some positive studies; as have the probiotic strains Lactobacillus casei and Lactobacillus rhamnosus.

State of the art care is to add a friendly yeast called Saccharomyces boulardii (by prescription: Florastor). The most current research supports the use of sporulating (A.K.A. soil-based) probiotics as well. These sporulating probiotics are potent, so watch your dose; starting as low as 5 billion and increasing to as many as 25 billion CFU’s (best done under a doctor’s supervision). These probiotics are species of Bacillus with b. subtilis and b. coagulans being the most studied. Finally, if you see your diarrhea disappear but still have gas and bloating studies are promising for using 10 billion CFU’s of Lactobacillus plantarum. If that doesn’t work, consider checking for SIBO; which I’ll discuss next.

Clear up Infections

If you have a history of vaginal yeast infections, you can easily get a cross-over infection in your gut. Small-intestinal-bacterial-overgrowth (SIBO) occurs when colonic bacteria “backwash” into the usually sterile jejunum. The most common yeast and SIBO symptoms are gas, bloating and constipation. Also, be aware of Helicobacter infections, and parasites. When in doubt, breath test, and treat.

Clear out Toxins

Common toxins that routinely “hit the gut” are mycotoxins (from mold), the dust mites that usually are not numerous enough unless there is “mold-food” for them and heavy metals such as mercury.

Toxins sometimes play more of a critical role in healing if you have difficulty in your detoxification (sulfation or methylation) pathways; something your doctor can test. High homocysteine, for example, means your methylation pathways need a boost. Having a few amalgam-based fillings isn’t usually “enough” to cause leaky gut. However, a steady diet of canned tuna-fish is actually enough to cause methylmercury build-up with effects on the gut and other organs.

Some practitioners tell patients to remove all amalgam fillings. Yes, all amalgam (mercury) fillings leech some mercury when you brush your teeth or chew your food. However, if you are acutely ill, this is absolutely not the time to start dealing with your fillings. First, get as symptom-free as possible, make sure your detoxification pathways are working well, and then find a biological dentist to (very carefully and slowly) remove your fillings if your doctor has tested you and found you to be mercury-toxic. As a ballpark number, this usually requires eight or more amalgam fillings.

Control Stress and Lower Cortisol

Stress is terrible for your health. We all seem to know that but do you know the physiologic reason why? When we’re talking about Crohn’s disease or any autoimmune disease, we’re looking at the direct effect high cortisol has on the gut. Sustained high cortisol can be the sole reason for having a leaky gut. This is the likely reason why so many bodybuilders (who all have high cortisol levels) have leaky gut.

Adrenal adaptogens, glandulars, and aromatherapy will go a long way towards lowering cortisol levels. Stress-busting techniques such as “vagal breathing,” meditation, and yoga in addition to other methods discussed on this blog will help too.

Balance your Hormones

The gut “works better,” and the microbiome stays more in balance when your hormones are in balance. A full discussion of this is beyond the scope of this article, but let me mention the two hormones which will slow gut motility (when they are low); cause SIBO and leaky gut. Low progesterone will cause a decrease in gut motility, constipation, and the whole nine yards. The same holds true with low levels of thyroid hormone. Obviously, when we talk about balancing and normalizing gut motility, we need to look at the hormonal “situation” as well.

Re-balance Gut Motility

As the gut lining becomes destroyed, some segments of the small and large intestine (depending on where the involvement of the disease is) get “out of sync.” As the gut heals, we sometimes need to use products to either bulk up the stool (modified citrus pectin) or improve GI transit at the smooth muscle level (by utilizing the serotonin precursor 5-HTP for example.) As mentioned, hormones need to be normalized as well. It’s strange to think a disease that produces “explosive” diarrhea can actually cause bloating and constipation while healing occurs, but this can happen. I recommend a multi-fiber blend which has prebiotic fiber and toxin-binding capacity to help with normalizing stool bulk, in addition to what I’ve already mentioned.

TNF-alpha Inhibition—A Cure for Crohn’s Disease?

First of all, know that the elevated levels of TNF-alpha start to come down with the interventions discussed above. Recall that “conventional medicine” offers Crohn’s patients “biologics,” which come with a wide range of potentially fatal side effects. I’m not saying they don’t work, and I certainly don’t suggest that you stop anything your doctor is prescribing. Note also the TNF-alpha inhibitors inhibit IL-6, and none of these drugs, nor what I’m about to share (or have shared) is curative.

However, if you implement all of the above steps, you will notice your symptoms significantly decrease or even disappear. Unfortunately, this is not a cure; but you can indeed get yourself into remission. If you’re on a “biologic,” ask if you can be weaned. Please make your doctor aware of what you are doing.

The following items have been discovered “in the lab” but were not tested on humans with diseases. We know that ketosis will inhibit TNF-alpha. Resveratrol, curcumin, melatonin, resveratrol, PQQ and vitamin D will also all inhibit TNF-alpha. We understand that some activities (ice baths, FIR saunas, and even cold showers, and baths) will suppress TNF-alpha.

Because the above practices are great for mitochondrial function and the above supplements are for mitochondrial dysfunction, it’s a no-brainer to recommend these supplements for most Crohn’s patients who all tend to have some fatigue.

In addition, there is new research brewing about low dose naltrexone that I find incredibly exciting. Of course, because pharmaceutical companies can’t figure out how to make a profit, it’s not mainstream discussion. But if you know anyone with Crohn’s disease or any autoimmune disease, I hope you’ll mention low dose naltrexone to them. If you have Crohn’s disease, I hope you’ll educate your doctor.


Low Dose Naltrexone

Why Researchers Were Interested

Around 30% of patients with inflammatory bowel disease (IBD) are resistant to all currently available IBD drugs, or they relapse over time. So, about 1/3 of all patients! Investigators with preliminary evidence as to the immune system improvement with low dose naltrexone recently investigated its direct effects on gut epithelial barrier function in a population of treatment resistance Crohn’s patients.

The study prescribed low dose naltrexone (LDN) to 47 patients who were followed prospectively for 12 weeks. Where available, endoscopic data including tissue biopsies were collected. In addition, the effect of LDN on wound healing (scratch assay), and other factors were investigated.

Low dose Naltrexone induced significant clinical improvement in 74.5%, and complete remission in 25.5% of patients. Naltrexone improved wound healing in epithelial (gut lining) barriers. Inflamed mucosa seen via endoscopy was reduced in all patients treated with LDN. From this study, researchers concluded that “low dose Naltrexone treatment is effective and safe, and should be considered for the treatment of therapy refractory IBD patients.”

Another clinical study involves 582 IBD patients. Among the 256 patients that became persistent LDN users, there were reductions in the number of users of all previously consumed drugs (-12%), intestinal anti-inflammatory agents (-17%), other immunosuppressants (-29%), intestinal corticosteroids (-32%), and aminosalicylates (-17%). Also, this study did not manipulate diet or use gut-healing agents and probiotics as you have read about in this article. Even this study’s researchers concluded that LDN reduced the need for toxic drugs in both Ulcerative Colitis and Crohn’s disease.

My Final Crohn’s Disease Treatment Recommendations

I’m not a fan of any “toxic drugs” for the treatment of Crohn’s disease. The right diet, pre and probiotics, supplements and low dose naltrexone for immune boosting and natural pain relief are quite compelling. At the moment, we can only obtain LDN from compounding pharmacies willing to use the standard 50 mg tablet and manipulate very low doses we need to treat patients. As the studies continue, we’ll see if this is a fluke (I seriously doubt it) or the silver bullet we’ve been waiting for.

UPDATE after 4/19 A4M meeting

In the discussion of peptides-the most exciting products to emerge on the regenerative medicine front, a potential OTHER silver bullet for Chrohn’s  patients was revealed. The peptide BCP-157 is not FDA-approved in the U.S. but many European doctors are finding that it does indeed heal intestinal mucosa. Stay tuned on this one!

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