Leaky Gut Diet: Which Diet Best Heals Your Gut?

By Amy Burkhart MD, RD

The connection between a leaky gut and chronic disease is undeniable, with the inflammation caused by leaky gut wreaking havoc on your overall health. But when it comes to the best leaky gut diet, the advice can be overwhelming and contradictory. With so many options, how do you know which foods truly help and which might make things worse?

Before diving into the best diet for leaky gut, let’s take a step back. What exactly is leaky gut, and what are its symptoms? Understanding the root of the problem is the first step to healing.

A healthy gut absorbs what we need and keeps out what we don’t.

The term gut refers to the digestive system, which includes everything from the mouth to the intestines, as well as organs like the gallbladder and pancreas that play a role in digestion.

When the gut is healthy, its lining acts as a gatekeeper, controlling what gets absorbed into the body. Some permeability is necessary—it allows nutrients to pass through so we can absorb the food we eat. But when the gut lining becomes too leaky, harmful substances slip through, leading to problems.

A weakened gut lining ( a leaky gut) —often caused by bacteria, toxins, or other irritants—allows unwanted particles to enter the bloodstream. Since these substances don’t belong, the immune system sees them as threats, triggering inflammation.

Chronic inflammation has been linked to conditions such as autoimmune diseases, IBS, and chronic fatigue.

The medical term for leaky gut is increased intestinal permeability—a condition that can have widespread effects on overall health.

Leaky gut can cause a wide range of symptoms, many of which overlap with other health conditions.

These may include:

• Digestive issues: Diarrhea, constipation, bloating
• Fatigue: Feeling constantly drained or low on energy
• Joint pain: Unexplained aches and stiffness
• Headaches
• Brain fog: Trouble concentrating or memory issues
• Skin problems: Rashes, eczema, acne
• Vitamin deficiencies: Poor nutrient absorption
• Muscle pain: Knots, tenderness, or fibromyalgia-like symptoms

Because these symptoms are non-specific and can be linked to many other conditions, a thorough medical evaluation is essential to determine whether leaky gut is the underlying cause.

Scientific evidence behind leaky gut

For years, there was debate over whether leaky gut was real. That changed in 2000 when Dr. Alessio Fasano and his team discovered zonulin, a protein that regulates the tight junctions—or “doors”—in the gut lining. Initially studied in people with celiac disease, zonulin was later found to play a role in gut permeability for many conditions.

Since 2001, research has linked leaky gut to inflammation and a variety of health issues, including IBS, depression, inflammatory bowel disease, and autoimmune disorders. This discovery has fueled growing interest in gut health, the microbiome, and their impact on long-term wellness.

However, leaky gut remains a controversial topic. There is no universally accepted test to measure gut permeability, and doctors typically diagnose it based on symptoms, which can vary widely from person to person. Some tests claim to assess gut permeability, but their accuracy is still uncertain.

Researchers are still exploring how gut permeability relates to symptoms and what treatments may help. While there’s no definitive evidence on how to fix a leaky gut, one thing is clear—chronic inflammation is harmful, and reducing it is beneficial for overall health.

Factors That Contribute to Leaky Gut

• Medications: NSAIDs (like ibuprofen) and proton pump inhibitors (PPIs)
• Stress & trauma: Can trigger or worsen symptoms
• Alcohol: Increases gut permeability
• Dietary triggers: Processed foods, sugar, gluten, and high-fat diets
• Microbiome imbalances: Caused by illness or antibiotic use
• Infections: Stomach infections like gastroenteritis
• Excessive exercise: Especially in endurance athletes
• Vitamin deficiencies: Low vitamin D levels
• Food additives: Such as carboxymethylcellulose and polysorbate-80
• Smoking: Negatively impacts gut health
• Obesity: Linked to increased gut permeability
• Low fiber intake: A fiber-poor diet can make the gut more vulnerable

Gut health is influenced by many factors, so addressing multiple aspects—like diet, lifestyle, and stress—can help support a stronger gut lining.

Reducing Inflammation: The Key to Healing Leaky Gut

Since inflammation worsens gut permeability, reducing it is the foundation of leaky gut treatment—especially while research continues to uncover the best ways to heal the gut.

From an integrative medicine perspective, addressing leaky gut goes beyond diet. It also involves improving sleep, exercise, stress levels, and mental health—all of which play a role in inflammation. By focusing on these areas, we can create a more balanced, gut-friendly approach to healing.

This article primarily explores the dietary aspect of leaky gut treatment. What you eat directly affects how permeable, or “leaky,” your gut becomes. Every food choice—today, tomorrow, and beyond—matters.

Chronic inflammation is linked to conditions like autoimmune diseases, anxiety, and depression. Taking steps now to adopt an anti-inflammatory diet and lifestyle can improve your long-term health.

To learn more, check out this study on how nutrition can support gut health.

Listed in alphabetical order, not the order of importance or recommendation.

The following are diets aimed at treating health and digestive problems. Many are also used by people to  “heal their leaky gut.”  Some have more research to back them than others.

The Autoimmune Protocol (AIP) is a diet designed to reduce inflammation, which is believed to be the root cause of autoimmune diseases.

Foods to Avoid on AIP

The AIP diet eliminates foods that may trigger inflammation, including:

• Dairy (including raw)
• Eggs
• Legumes (beans, peanuts, hummus, etc.)
• Refined sugars
• Processed foods
• Industrial seed oils (vegetable oil, canola oil, etc.)
• Grains
• Nuts and seeds
• Chocolate
• Nightshade vegetables (tomatoes, peppers, potatoes, eggplant)
• Alternative sweeteners
• Food additives (gums, thickeners, and emulsifiers like xanthan gum and guar gum)

Foods Allowed on AIP

The AIP diet focuses on nutrient-dense, anti-inflammatory foods such as:

• Lean meats and organ meats (such as liver)
• Fermented foods
• High-quality seafood
• Vegetables (excluding nightshades)
• Fruit (in moderation)
• Healthy fats (olive oil, coconut oil, avocado oil)

Does the AIP Diet Help with Leaky Gut?

The AIP diet aims to calm the immune system and has been used to support conditions like inflammatory bowel disease. The benefits are promising as it does appear to lower inflammation. The diet is highly restrictive.

The anti-inflammatory diet is well-known for its ability to reduce inflammation.

It focuses on:

✔ Fresh, whole foods
✔ Healthy oils and fats
✔ Low sugar intake
✔ More fish than meat
✔ Plenty of fruits and vegetables

Not only is it a nutritious way to eat, but it’s also realistic and sustainable for long-term health.

While its direct impact on gut permeability hasn’t been studied, the diet is rich in foods known to lower inflammation, which may support overall gut health.

An elemental diet provides essential nutrients—proteins, fats, and carbohydrates—in a pre-digested form, meaning the body doesn’t have to break them down. This allows the digestive system to rest and heal.

Key Facts About the Elemental Diet:

• Primarily used for chronic digestive conditions under medical supervision
• Available as a liquid or powder that mixes with water
• Can be store-bought or homemade
• In severe cases, it may be administered through a feeding tube when oral nutrition isn’t possible.

Who Might Benefit?

The elemental diet is often used for conditions such as:

• Ulcerative Colitis
• Crohn’s Disease
• SIBO (Small Intestinal Bacterial Overgrowth)

Research suggests that the elemental diet can help improve leaky gut, making it a potential therapeutic option for those with gut-related issues. This diet should be followed under the guidance of a healthcare provider.

If you suspect celiac disease, it’s essential to get tested before starting a gluten-free diet to ensure accurate results.

What Is a Gluten-Free Diet?

A gluten-free diet eliminates all foods containing:

• Wheat
• Barley
• Rye
• Oats (unless certified gluten-free)

This diet is the only treatment for celiac disease and is also used by people with gluten intolerance (gluten sensitivity).

Does Gluten Cause Leaky Gut?

• Research confirms that gluten can trigger a leaky gut in people with celiac disease.
• However, despite what you may read online, there is no proven evidence that gluten causes leaky gut in everyone.
• Studies show that gluten increases gut permeability in those with celiac disease and gluten intolerance.
• A low-gluten diet has also been linked to reduced inflammation.

While avoiding gluten may benefit those with sensitivities, more research is needed to determine its effects on gut permeability in the general population.

Intermittent fasting (IF) has gained popularity for its many health benefits.

What Is Intermittent Fasting?

There are several types of IF, but the most common is the 16:8 method, where you fast for 16 hours and eat within an 8-hour window.

How Does It Affect Gut Health?

• Intermittent fasting has been proven to lower inflammation 
• Research suggests that alternate-day fasting and time-restricted eating may strengthen the gut lining, reducing permeability and making the gut less leaky.

While IF offers promising gut health benefits, and it does decrease inflammation, there are no direct studies on gut permeability and intermittent fasting. Please check with your health care provider before using IF.  Intermittent fasting is not suitable for everyone.

The ketogenic diet (or keto) was initially developed to treat seizures.

What Is the Ketogenic Diet?

A keto diet is very high in fats and very low in carbohydrates and protein. Normally, our body uses glucose (a type of sugar) as its main fuel source. However, when glucose is scarce—like on a low-carb diet—the body produces ketones as an alternative fuel.

These ketones not only provide energy but also help suppress hunger. Ketosis (the state the body enters when burning ketones for fuel) is a natural survival mechanism that helps us cope with food shortages.

Keto and Gut Health

• Initially used to treat epilepsy and seizures, the ketogenic diet is now widely popular but can be restrictive and challenging to maintain long-term .
• The keto diet may alter the types of bacteria in the gut and potentially reduce inflammation.

While keto may have benefits for certain conditions, however, there are no direct studies linking the ketogenic diet to gut permeability as of now.

The low FODMAP diet is used to treat IBS.

What Are FODMAPs?

FODMAP stands for a group of carbohydrates that can cause symptoms like diarrhea, stomach pain, and bloating in some people. These carbohydrates are naturally found in many foods, even healthy ones like onions, apples, and garlic.

It can be difficult to know which foods contain FODMAPs, so it’s helpful to get guidance from a healthcare provider. Apps can also help identify FODMAP foods.

How Does the Low FODMAP Diet Help?

• Most research on the low FODMAP diet has focused on reducing symptoms like gas and diarrhea.
• One study showed that the diet might also help reduce leaky gut and improve gut function. This could be due to changes in which bacteria are thriving in the gut.

While the diet has helped many people with IBS, further research is needed to better understand its direct effects on the gut lining.

The Mediterranean diet is easy to follow for most people

The Mediterranean diet is a specific anti-inflammatory diet based on a high intake of whole fruits and veggies, olive oil, and a low intake of sweets, meat, and alcohol. The focus is on fish and beans and minimal red meat for protein.

The Mediterranean eating pattern is protective against many diseases, including cancer and Alzheimer’s. It may also help prevent and treat IBS symptoms. It’s relatively easy to follow. Fewer foods are eliminated, and many cookbooks and blogs have recipe and menu ideas.

Studies have shown that the more closely a person follows the Mediterranean eating pattern, the fewer IBS symptoms they have. The Mediterranean diet can lower inflammation. Few studies are looking specifically at the Mediterranean diet and leaky gut.

There are several variations of the paleo diet.

The Paleo diet is based on the idea of eating the way our ancestors did, before farming and industrialization. It focuses on lean meats, fruits, vegetables, and nuts, while avoiding foods like grains, legumes, and processed foods that contain additives

Foods Typically Eliminated on the Paleo Diet:

• Dairy (though some versions allow it)
• Legumes (e.g., beans, peanuts, hummus)
• Refined sugars
• Processed foods
• Industrial seed oils (e.g., vegetable or canola oil)
• Grains

Foods Permitted on the Paleo Diet:

• Meat and fish
• Eggs
• Nuts and seeds
• Fruits and vegetables (but no corn)
• Healthy fats (e.g., coconut oil, olive oil, avocado, lard, ghee)
• Minimally processed sweeteners (e.g., raw honey, maple syrup, coconut sugar, raw stevia)

Some Paleo bloggers and cookbook authors have a more flexible approach, including recipes with added sugars, claiming they are healthier since they’re less processed. However, the body doesn’t distinguish between different types of added sugars. What matters most is not overeating sugar, no matter the form, as sugar can cause inflammation.

The Paleo diet helps eliminate many foods that promote inflammation and has been shown to lower inflammation. However, there is no direct research on how the Paleo diet affects gut permeability.

The Specific Carbohydrate Diet (SCD): Reducing Inflammation, but Challenging Long-Term

The Specific Carbohydrate Diet (SCD) has been used for nearly 100 years. It was originally developed by a physician to help her child with celiac disease, and today it is used for various conditions, including inflammatory bowel disease 

Despite its name, the SCD is not a low-carbohydrate diet. Instead, it focuses on eating simple carbohydrates that are easy for the body to absorb. The diet eliminates:

• Grains
• Milk (except for hard cheese and yogurt)
• Sugar, except for honey

There is some overlap with the low FODMAP diet .

While research shows that the SCD diet can improve IBS symptoms, there is no direct research on how it affects gut permeability. However, studies have demonstrated that it can lower inflammation.

The program eliminates added sugar, additives, grains, alcohol, dairy, and legumes for 30 days.

The Whole30 is based on a well-known elimination diet principle:

• Remove foods that may be causing symptoms.
• Nourish your body with whole foods rich in fiber, vitamins, and minerals for 30 days.
• Reintroduce eliminated foods one by one and observe any changes in how you feel.

Although there are no specific research studies on the Whole30, it has gained popularity, with many cookbooks, approved brands, and blogs supporting the journey.

By eliminating processed foods, alcohol, and sugar, the Whole30 could potentially help reduce inflammation, even if studies on the diet itself are lacking.

Lifestyle changes to help you heal and feel great

1. Decrease stress; stress can cause unwanted changes in the gut microbiome
2. Exercise 30-60  minutes daily; exercise has a positive effect on the gut and the microbiome
3. Sleep 7-9 hours a night; sleep has a positive effect on the microbiome
4. If possible, avoid medications that worsen leaky gut
5. Treat underlying medical conditions
6. Maintain a healthy weight; obesity is linked to inflammation in the gut
7. Don’t smoke
8. Avoid or limit alcohol; alcohol increases inflammation in the gut
9. Maintain normal vitamin D levels – if you don’t know yours – check! Low vitamin D is associated with gut inflammation.

Many of the diets listed above lower inflammation and have been directly linked to lowering gut permeability/leakiness. With this in mind, the best “diet” for ‘leaky gut” is one that fits your individual needs and lowers inflammation and leaky gut symptoms. And has the following characteristics:

• Is the least restrictive
• Can be followed long-term
• Focuses on real food and contains predominantly plant-based foods (if tolerated)
• It is high in fiber.
• Limits or eliminates processed foods such as chips, cookies, pretzels, etc.
• Eliminates foods you may react to, as determined by an elimination diet if necessary
• Limits or eliminate added sugar as found  in candy, cakes, juices, sodas
• Looks closely at common offenders: dairy, FODMAPs, nightshades, sugar, and gluten. Not everyone reacts to these foods. They are common triggers that may need to be eliminated or reduced.

Dr. Burkhart’s Final Input

• Direct Connection: Most of the diets discussed have not yet proven a direct link between leaky gut and intestinal permeability. That doesn’t mean the connection doesn’t exist. Research often lags behind real-life experience.
• Clinical Judgment: If a treatment helps someone feel better and isn’t harmful, I trust clinical judgment to guide decisions. Medicine is not perfect.
• Inflammation is Harmful: Whether or not you believe in “leaky gut” as a disease process, it’s clear that inflammation is harmful. Any diet that can reduce inflammation is beneficial.
• Restrictive Diets: I don’t recommend sticking to highly restrictive diets long-term unless medically necessary. These diets can make it hard to maintain emotional and physical health, and the risks and benefits must be carefully considered. Professional guidance may be needed.
• The Ultimate Goal: The goal is to find the least restrictive, least inflammatory diet possible. Eliminating certain foods may not be permanent. With the right diet and lifestyle changes, we can improve gut health, enjoy a wider variety of foods, and achieve better overall health.