Is Heartburn Caused By “Leaky Esophagus”? | Chris Kresser

Is Heartburn Caused by “Leaky Esophagus”?


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Reflux isn’t caused by having too much stomach acid, and acid-suppressing drugs miss the mark when it comes to treatment.

leaky esophagus and heartburn
There may be a connection between leaky esophagus and heartburn. magnettheory/iStock/Thinkstock

Heartburn, also called gastroesophageal reflux disease (GERD), is the most common digestive disorder in the US, and the acid-suppressing drugs used to treat it can have dangerous side effects after long-term use.

The prevailing belief by the public, and even many conventional doctors, is that reflux is caused by having too much stomach acid, hence the standard treatment with antacids and PPIs. But we now know that GERD is not a disease of excess stomach acid, and many GERD patients actually produce lower levels of stomach acid than normal.

In light of this evidence, it seems logical that heartburn must be caused by stomach acid inappropriately entering the esophagus. And indeed, tests for esophageal acid contact time have confirmed that most patients with heartburn and GERD do have above-normal acid contact time over a 24 hour period. (1)

As I’ve discussed in the past, one cause of increased acid reflux into the esophagus is dysfunction of the lower esophageal sphincter (LES), a valve that separates the esophagus from the stomach. This dysfunction can be caused by increased intra-abdominal pressure, which often results from bacterial overgrowth in the small intestine. This has been one of the prevailing theories about the underlying cause of reflux for several years now, but it has some limitations.

Not All GERD Patients Have Abnormal Amounts of Acid Reaching Their Esophagus

As I just mentioned, most GERD patients do have above-normal acid contact time. But most is not all. In fact, 24-hour acid contact tests have found that up to 30% of GERD patients actually have normal acid contact time. (2, 3)

Some patients with GERD symptoms even have normal endoscopy results – their esophagus looks the same as a healthy person’s esophagus. These patients are considered to have ‘non-erosive reflux disease,’ or NERD, and up to half of NERD patients have normal acid contact time. (4)

So, what separates a healthy individual from a GERD or NERD patient with normal acid contact time? If there isn’t too much stomach acid reaching the esophagus, what is causing the heartburn?

One theory gaining traction in the scientific community to describe this phenomenon is the idea of impaired epithelial barrier function. In other words – GERD might be a result of “leaky esophagus.”

Is a “leaky esophagus” the cause of your acid reflux? #gerd #heartburn

What Is “Leaky Esophagus”?

You’ve probably heard of “leaky gut” before. Cells in the epithelial lining of the intestine are held together by tight junctions, and if these tight junctions are disrupted, particles that wouldn’t normally be absorbed make their way through the lining of the intestine and into the bloodstream. This can cause a host of problems, from food allergies to autoimmunity and more.

“Leaky esophagus” is a similar concept. It’s actually normal for acid and stomach contents to reflux into the esophagus occasionally. (5) In a healthy esophagus, this acid can’t penetrate the cell membrane of the epithelial cells, and tight junctions prevent it from getting in between the cells.

In fact, normal esophageal tissue is remarkably resistant to acid. In acid perfusion (or “Bernstein”) tests, acid is dripped directly onto the esophagus through a tube that is inserted through the nose (sounds pleasant, right?), and healthy people don’t experience any pain or heartburn, even after half an hour. (6)

However, if those tight junctions are disrupted, acid can make its way between the epithelial cells, decreasing the pH of the intercellular space. Since even small pH changes in this area are threatening to the body, there are pain receptors located close to the epithelial lining, and they send pain signals to the brain in response to the lower pH. These signals are interpreted by the brain as heartburn. Unsurprisingly, patients with NERD or GERD who receive the Bernstein test experience discomfort almost immediately.

As further evidence of the presence of leaky esophagus, biopsies of GERD and NERD patients almost always reveal dilated intercellular spaces, which is a marker for impaired barrier function. (7) These dilated spaces are increasingly being accepted as a hallmark symptom of both NERD and GERD.

Is Leaky Esophagus a Cause or a Symptom of Reflux?

It appears that leaky esophagus is present in most cases of GERD. But it’s not clear whether leaky esophagus is a cause of reflux, or just another side effect.

Even though a healthy esophagus is resistant to acid, high levels of acid exposure over time will eventually lead to inflammation and impaired barrier function. In this case, increased acid exposure comes first – most likely due to a dysfunctional LES – and leaky esophagus is not the root cause; it’s just another symptom.

However, there maybe some reverse causality, particularly in GERD patients who have normal acid contact time. In this case, something other than acid exposure disrupts the epithelial tight junctions, which causes heartburn even at normal acid levels. Over time, this “leaky esophagus” can lead to the visible epithelial tissue damage observed in GERD patients.

This happens because the “back” side of an epithelial cell is not as resistant to acid as the “front” is, so once the acid seeps through the tight junctions, it can enter cells from the back and cause cell death and tissue damage. (8)

Unfortunately, this process can actually lead to LES malfunction and increased acid exposure, creating a vicious cycle. Now, increased acid exposure in the esophagus is a symptom of GERD, rather than the root cause.

What Causes Leaky Esophagus?

So if leaky esophagus happens first in some cases of GERD, what causes leaky esophagus in the first place?

One possibility lies in the esophageal microbiome. The esophagus houses a community of microbiota similar in complexity to the intestinal microbiome, and the makeup of this bacterial community is different in healthy people compared to people with GERD. The microbes found in the esophagus of GERD patients are primarily gram-negative, while the microbes in the esophagus of healthy people are primarily gram-positive. (9)

Increased numbers of gram-negative bacteria can trigger inflammation by exposing epithelial cells to lipopolysaccharides (LPS), a component of gram-negative bacteria that causes immune responses in the body. (10) The inflammatory cytokines released in response to LPS can then lead to loss of tight-junction integrity, resulting in esophageal permeability. (11, 12)

Exposure to LPS can also cause the LES to relax, promoting reflux and increasing acid exposure time – again, creating a vicious cycle. (13)

Unfortunately, there isn’t a lot of research yet that clarifies the causes of increased esophageal permeability. But if the mechanisms at work in the esophagus are similar to those in the intestines, other probable causes could be stress, excessive alcohol consumption, and excessive use of non-steroidal anti-inflammatory drugs (NSAIDS). (14, 15, 16, 17)

All of these factors can contribute to leaky gut, so it wouldn’t be surprising if they contributed to leaky esophagus as well.

What Does This Mean for Heartburn Sufferers?

As you can see, GERD is a complex and multifaceted disorder with no single cause or presentation. Luckily, all of the strategies for healing heartburn and GERD that I’ve been recommending for years would also be expected to heal leaky esophagus.

A low-carb Paleo diet, gut-healing foods like bone broth and fermented foods, regular stress-management, and a focus on balancing the intestinal (and esophageal) microbiome with probiotics and prebiotic foods are always good approaches to treating the root cause of GERD.

Now I’d like to hear from you. Have you cured your heartburn using a Paleo diet? What other strategies have worked for you? Share your story below!


Join the conversation

  1. My GI specialist has been confirming I have GERD and chronic gastritis for more than 6 years doing and endoscopy every 3 to make sure no cancer. He has never told me why I have this problem or cause and tells me to take more medication. I started The Plan diet in Jan and consulted a functional medicine Dr and with her help supplements and food testing through the plan I can pinpoint my reflux causing foods and have quit taking my medications. When I’m not careful I get it back instantly but I try to be extra careful

  2. I have had HORRIBLE LPR(acid reflux) for years and was taking up to three aciphex a day, zantac, Pepcid, etc… to try to alleviate aerolisized acid in my upper digestive tract(what felt like gases). At times it was so bad that I couldn’t eat and lost 15-20 lbs. After the “best” doctors and medical institutions across the country and thousands of dollars later I met with a functional medicine physician–neurologist and nutritionist–who recommended the book, Primal Body, Primal Mind. I discontinued all ppi’s and have eliminated carbs(roughly below 50 grams/day) and have eliminated the majority of the “gases”. Also, was diagnosed with sibo…and

  3. I have a somewhat different issue. I was told that I have a hiatal hernia based on an X-ray that was taken of my torso after my first (and only) bout with diverticulitis. I rarely have heartburn or reflux, but I do have a chronic cough that brings up phlegm. I don’t eat grains or gluten, and have been low-carb/Paleo since 1998. I take daily prebiotics and probiotics along with digestive enzymes. Anything else I can do?

    • I had a break out of acid reflux a few months back. My nurse practitioner (who uses functional medicine as the basis for her practice) suggested that I be checked for a hiatal hernia. I went to my VERY alternative chiropractor, he checked and said indeed I did have one. He performed a quick manipulation to correct. it. I was out of there and haven’t had any problems since.

  4. I have crohns although I don’t take any medication and control it through diet
    I sometimes get heartburn after excercise
    Are the 2 related what can I do to prevent it ?
    Should I be taking a probiotic

  5. I have ‘silent’ reflux I am told. No heartburn but symptoms of sore throat, persistent cough & occasional voice alteration. Endoscopy normal. I was on higher dose ppi’s for 3 years & symptoms went away. However a second dexa scan (I am aged 68) revealed that during this time I had lost 10% of my bone density and now have severe osteoporosis (for which I have refused to take alendronic acid but that’s another story).
    I believe that taking the ppi’s caused reduced mineral absorption (I’ve read quite a bit about the possibility of this effect) so I weaned myself off the medication (stopping abruptly made it worse).
    I also do several things to help myself with reflux (making kefir, sauerkraut, low gluten, not eating or drinking within 3 hours of bedtime, sleeping on a wedge for eg) but I cannot do low carb, I just lose weight & am underweight as it is (which isn’t good for bone density). However I am coping & wanted to warn people about taking ppi’s and their effect on bone density. Thank you very much for your articles, they are really helpful.

  6. Chris, this i amazing info! I have found one really interesting observation. Whenever I get on a very low carb, low fiber diet, I start getting urinary tract infection, when i increase carbs, it goes away. So my theory is that gut microbiome affects all other microbiomes directly. Like esophagus, urinary tract, lungs, and everything else. Is that documented in scientific literature? I think it c

    • I think it could also explain why ketogenic diets increase your risk for serious infections like pneumonia.

    • Yes, there is evidence to support the connection between the gut microbiome and other microbiomes like the skin, lungs, urinary tract, and even nasal passages. For example, I recently came across a study showing that oral probiotics can be helpful for chronic sinusitis sufferers.

  7. Just a thought- you know how you recommend increasing stomach acid in your GERD series….but if these patients have other mechanisms for esophageal disease, as listed in that 2013 review article, aren’t you just going to matters worse by increasing the acid exposure of an esophagus which already has integrity problems??

    • In these cases they will almost always feel worse taking HCL, which is why I recommend stopping if that happens.

  8. TYPO –
    “However, if those tight junctions are disrupted, acid can make its way between the epithelial cells, decreasing the pH of the intracellular space. ”
    I think you mean “intercellular space”
    Thanks for presenting a new conceptualization of GERD.

  9. Cured my acid reflux by taking HCL tablets. They Improved my digestion as well. Win win. Tried them after reading that some acid reflux sufferers actually have low stomach acid levels. its often acid in the wrong place that’s the problem rather than too much.

  10. Hi Chris,
    As a clinical Nutritionist, I have used a low carb high plant-based raw food diet to treat myself of chronic acid reflux, as well as using the same dietary approach with clients suffering the same problems. Your theory seems quite plausable, one that had not crossed my mind till now.
    My reasoning for a plant -based diet was to get a higher level of digestive enzymes into the body that would aid in the its ability to breakdown food particules.
    My clients have reported that if they ended their day with a salad, rather than a snack or meal their symptoms were greatly reduced or removed.

    • I have found that if I vary from my mostly Paleo diet and have – say – two pieces of gluten-free bread at dinner, I’m woken up by that ghastly acid coming up the throat. It’s no longer worth it to me. But I never get that reaction if I stick with a non-grain diet. The whole “acid reflux” thing seems to be due to the amount of grains we are eating these days.

  11. I had a complete cure from day ONE on a very low carb diet after 15 years on increasing daily doses of PPIs. I took a good probiotic concurrently – 10, 000, 000 per capsule per day. Thanks Chris, Rob Wolf, Jimmy Moore, Gary Taubes – all of you! Both me and my man – who had more severe gut issues than me – are medication free and feeling fab in Geneva! THANKS!

    • My boyfriend also took PPIs for 15 years. When we both went on a Whole30 (his first time), he had no need for Prilosec starting at Day One. After one week, the feeling of esophageal tightening he had when drinking fluids went away as well. At the end of the 30 days, we’ll add back foods one at a time as recommended in Chris’ book to see what his specific triggers are. He was amazed at the “miraculous” cure!

  12. Hi Chris, thanks for this new insight.
    I was diagnosed with GERD some four to five years ago when the cyclical episodes of burning pain accompanied by a dry cough was the evidence for the diagnosis.
    I was prescribed a rather expensive medication to stop the reflux (inhibit the HCL) but instead I trawled the internet for clues about a natural remedy.
    I self treated with Apple Cider Vinegar, believing that I had a diminished HCL due to my age, and coincidentally stumbled across the Paleo lifestyle.
    Now after nearly three years of Paleo, a change of lifestyle which also includes regular ACV, my GERD has completely disappeared.
    I am very grateful for all the info. Thanks Chris.

  13. What is “acid contact time”?

    I’m on Pantozol for 16 years now after I got stomach pain when taking steroids for my arthritis. Any time I try to get rid of Pantozol I get bad stomach pains again. Any idea how to get rid of this medication?

  14. Hi Charis, I agree with you and facing similar problems. Could you advice what typical foods to be taken to avoid this also any medicine to control bacterial overgrowth

  15. Wow….that was all so good to read, thank you!! I discovered accidently that excluding wheat and sugars from my diet solved my reflux issue…..I only get it now if I eat a small packet of innocent (not!) biscuits. Who would have thought, so simple. Fermented sourdough rye/oat bread occasionally does not cause me any discomfort btw.


  17. Interesting article. I have a burning sensation in the throat after eating and at other times of the day. A 24 hour test showed acid exposure normal and manometry also normal. So I am told I don’t have reflux despite the burning symptoms. How does one get a diagnosis of NERD? Sounds like my symptoms could be NERD though, and leaky esophagus could be behind it? I also have SIBO diagnosed through breath testing and IBS, and most likely leaky gut, so a disrupted microbiome in the esophagus doesn’t sound unlikely.

  18. I had GERD a few years ago, and tried a few strategies before going on drugs. Found trigger foods such as caffeine, tomatoes. When I gave up gluten and went paleo, the symptoms disappeared almost overnight, and within a week was sleeping flat and ditched the drugs. it was an amazing vindication of the absolute importance of the role of inflammation. Now after a recent flare that finally diagnosed my Hashimotos, (I finally found a doctor that could join the dots) all the pieces of the puzzles are becoming apparent. Though everyone is different, I agree that the only way forward with these complex and distressing conditions is strict Paleo, with all its facets of stress management, sleep, sunshine and activity in place. Its hard at times to keep all those balls in the air, but I encourage anyone thinking about change to have a good hard go at it, as it could give you your life back!

  19. Classic example of how Big Pharma over influences the practice of medicine, especially in the USA. I was diagnosed with GERD in 1984 (in Australia) by a gastroenterologist. She explained about the esophagus and suggested a lower fat diet (bacon and chocolate etc used to trigger pain). All my Sx went away when I went on my diet for Lupus in the late 80s (what they now call the AIP). But clearly since then more drugs have been developed and pushed.

    BTW, I had a friend whose tiny (almost newborn) infant had reflux and who was prescribed acid reducing medications. She was breastfeeding. This horrified me at the time. reading the research and Chris’s analysis, I feel even more vindicated.

    • It has been a long time since I had contact with an infant.

      As I recall, it IS common for babies to “spit up”. That is partly what burping them is about.

      I am glad PPI’s were not on the market then. I might have been tempted. Today, I would not be.

  20. Great info, thanks. How about someone who has both GERD and histamine problems though? The suggestion of eating fermented foods still stands?

    • i had GERD so bad anything i ate or drunk gave me severe acid pain throughout my torso.
      I took L Glatamine powder daily, this repairs Leaky Gut tissue.
      Since then i can eat whatever i like w/out any acid pain at all.
      If it comes again just repeat the L Glutamine.
      What you think to this Chris ?

    • Probably not, until you address the histamine issues. Probiotics that include species that aren’t histamine producers would be better.

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