How Sleep Apnea Causes Pepsin Reflux

November 9, 2009

Sleep apnea and acid reflux go hand in hand. An obstruction causes a vacuum effect in the throat, which suctions up your normal stomach juices into your throat, causing more inflammation and swelling, causing more obstruction. If you have large tonsils, it becomes even more enlarged, causing severe breathing problems at night. Not only do the mucous membranes of the throat become swollen, the tongue swells up as well, leaving impressions on the sides of your tongue due to pressing on the teeth.


Most people are aware of acid reflux, but what’s virtually ignored is the fact that your stomach juices contain many other irritating substances, including bile, digestive enzymes, and bacteria. In fact, pepsin, one of the main digestive enzymes, and H. pylori, a common stomach bacteria, are both found in ear, sinus and lungs washings. These are major sources of inflammation and swelling in your upper airway.


A recent study published in Otolaryngology – Head & Neck Surgery showed that deposits of pepsin can linger in the throat, and every time acid comes up, it gets activated in the more acidic, low-pH environment. They cultured throat cells with and without pepsin and measured 84 different inflammatory markers, of which 9 were found to be significantly increased, even in a non-acidic environment. This can potentially explain why people with laryngopharyngeal reflux disease have persistent symptoms despite maximal acid reflux medication therapy. 


Laryngopharyngeal reflux disease is a common condition where small amounts of stomach juices reach the throat. But it’s important to realize that giving acid suppressing medications like Nexium or Prilosec does nothing to prevent reflux. What these medications do is to lower acid production in the stomach so that whatever comes up doesn’t irritate the throat (or esophagus) as much. It’s not surprising that these medications don’t always help.


I think you’ll agree that constantly having small amounts of digestive enzymes in your throat can definitely cause problems. More commonly, people will complain of post-nasal drip, throat clearing, hoarseness, chronic cough, a lump sensation, tightness, burning, usually with no stomach problems whatsoever.


This is why eating early and not snacking before bedtime is so important for people with sleep apnea (and everyone else, too). 


Do you have to clear your throat constantly, or have post-nasal drip, chronic cough, or hoarseness? Please enter your experiences below in the comments box.

30 Responses to “How Sleep Apnea Causes Pepsin Reflux”

  1. Paula Brannon on November 10th, 2009 9:45 pm

    Great article! But, does the sleep apnea cause the acid reflux, or amplify it? I have sinus congestion, acid reflux, and recently diagnosed with sleep apnea. My tonsils have “grown back” after 40 years. I can’t get off the Prilosec, but have gotten off one of my high blood pressure medications. Will my acid reflux eventually stop because I’m on a cpap? It’s like hot knives cutting through my throat.

    Thank you,


  2. Steven Park on November 11th, 2009 3:57 am

    It doesn’t matter which comes first. Once it starts, it’s a vicious cycle. Treating sleep apnea should help with your laryngopharyngeal reflux disease, but don’t count on curing it completely. You may need to stay on Prilosec for a while until things settle down and then consider tapering off once you feel better. Thanks for commenting.

  3. Robin on November 24th, 2009 6:53 am

    I was diagnosed with pharyngeal reflux disease almost 4 years ago. I had been to my GP, and allergist when I was sent to an ENT. I had laryngitis for 6 months (no kidding) and it was really tough. I sing, and I am an educator, so I use my voice a lot. The protonix worked really well for about a month, but then symptoms started to return. It is so frustrating…my singing voice and range have been affected most of all. I have real difficulty with the transitions that are right aroune my lift-point (where I change from my “chest voice” to my “head voice”) I don’t know what else to do. I have gone to a new ENT, and he has ordered a video strobe test(?) So, here we go again. Do you have any suggestions?

  4. Steven Park on November 24th, 2009 7:58 am


    Your experience is not too surprising. Protonix and other acid relfux medications don’t prevent your stomach juices from reaching your throat. Are you absolutely avoiding eating or drinking alcohol within 3-4 hours of bedtime?

    Do you have any other symptoms of an underlying sleep-breathing disorder such as unrefreshing sleep, not being able to sleep on your back, and maybe even snoring?

    If some of the above problems resonate with you, I recommend that you read my book, Sleep, Interrupted. It describes my sleep-breathing paradigm, and steps you can take from conservative to more aggressive steps.

  5. kevin Mailey on March 11th, 2010 6:09 pm

    I have sleep apnea  and acid reflux  and it can be difficult to use machine sometimes I thin k I could use the cpap if i had the reflux under control  but as it stands it hit and miss every night whether I get sleep or not its wearing me down   I have started to use Kangen Water to see if it can help whats u opinion  I would try anything

  6. keri on March 25th, 2010 10:08 am

    i recently in nov or so started thinking i had to clear my throat because of allergies which i treated to dry up..then in jan it got worse more stuff in throat to clear and my anxiety started up so i dont know if one fuels the other..i know if im more relaxed the throat wont flare but something is their even with anxiety..ive tried so many natural treatments one by one dont know if there working or not..but ill try anything..i feel a little burning in my stomach here and there but just the do u really treat this..ive checked my ph which was 6 but then 7.5 so is that a true test of really concerned it wont go away..what do i do to fix this? i dont eat wrong foods.drink alcohol or smoke..

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  8. Michael Dilday on December 4th, 2010 9:36 pm

    I have been dealing with reflux for several years. Constant pain in my throat right side at the top of my collar bone – when I breathe outside in the cold or inhale after chewing a halls I can feel the pain sensation down there. I switched from prilosec to nexium and zantac about a month ago. I have a follow-up visit with my gastroentorologist next week. My wife says I snore very loudly. I also have pain where my left nostril connects to my throat but this has improved greatly.

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  10. Steven Park on December 6th, 2010 8:03 am


    It doesn’t matter which comes first. Ultimately, it’s a vicious cycle. Reflux from sleep apnea can cause your tonsils to get larger, which causes more sleep apnea. Assuming your CPAP is being used effectively, your throat problems should improve. Good luck.

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  15. Heather on January 18th, 2012 5:13 pm

    I am in the same boat as many. I have had reflux for over 4 years, and have now been told I have sleep apnea. I definately feel the 2 conditions make the other worse. I have tried the reflux medications-they dont work for me. I was told my tonsils are large and my tongue sits too high. I have propped up with pillows at night to sleep but think my next step is elevating the head of the bed itself. If that doesnt work I may consider having some of my soft tissue removed. I go home each day at lunch and power nap for 15 minutes just to work an 8 hour shift. yuck . I don’t go out anymore on the weekends because that is my sleep time. My friends make fun of me for “being old and tired. ” Its not funny.

  16. Liz on March 22nd, 2013 10:34 am

    I had a severe bout of acid reflux post surgery a couple of months ago. Then I developed a problem swallowing liquids; they feel like they are going back up through my nose, and my palate feels swollen. My nasal passages/sinuses feel irriated all the time. I had an esophagram a couple of days ago and it showed no abnormality with swallowing. An ENT exam also showed no abnormality, except for some redness. I am on a dose of Zantac at night, which helps the GERD but it’s not gone completely. I need to find out what is causing this as it is very distressing.

  17. fran simko on May 7th, 2013 12:53 am

    Don’t know if its allergies or what I read above, but I am always clearing my throat, possibly due to post nasal drip. I haven’t experienced acid reflux issues at this time. I am in the sleep field, and find this information to be very interesting. Most people that have a sleep study almost always experience gerd.

  18. mark plaaitjies on October 15th, 2013 2:04 am

    Just been diagnosed with OSA, i have GERD, constant post nasal drip, tired during the day, cant do anything, no drive for anything, i stopped all activitites, i work eat and sleep thats all, i have no life left, im always miserable and depressed or sad. OSA has taken over my life in a big way, im only surviving due to my wife and daughters otherwise, i would not able to continue living this way. I gather that the CPAP machine is also not great to use, im hoping that the med aid pays for it so i can alteast have a little better quality of life, forking all those thousands is making me feel even worse.

  19. Kevin Brooks on December 15th, 2013 10:55 pm

    I have been trying to get what I now think is LPR diagnosed for the past 3 months. Originally it started out as a sore spot on my lingual tonsil. I visited 2 ENTs and they kept giving me antibiotics and antihistamines. I began to freak out a bit and thought it might be tongue cancer. After stressing, a few weeks later the dry cough, hoarseness, etc. showed up. I have had these symptoms for about 3 weeks now and after doing my own research I am pretty sure it’s LPR. I am getting an ECG this week to see if there is any structural damage to the Oesophagus.

    Any suggestions for getting rid of the Pepsin? I have read that alkaline water works. I don’t really want to take any meds. I just put myself on a strict diet as well. Suggestions for sleep apnea? I do have a deviated septum. Should I get that surgically fixed?



  20. M Douglas on December 25th, 2013 6:04 am

    I am scheduled to go in for a second sinus surgery on Friday. I was told by my ENT that my sinuses are so bad that they are siphoning my stomach acid up into my throat which causes horrible and uncontrollable coughing. I am taking protonix but none of the stomach meds I have taken are helping at all. I have been trying to research this condition online but cannot find anything. What have you heard or know about this specific problem.
    Thank you,

  21. Cindy on January 2nd, 2014 10:03 pm

    A sleep study has indicated that I have many obstructive episodes but no ‘apnea’ per se. Right now one of the most disturbing symptoms I have is a burning of my tongue & the roof of my mouth. This can occur at anytime of the day, but is most noticeable (& most troubling) upon awakening in the morning (or when lying down to sleep).

    I do not have burning in my throat or in my stomach.
    The sides of my mouth though can also sometimes be affected with this burning sensation. I am wondering whether there are glands that secrete acids in the mouth, I would think so, as part of the normal digestion process. But why would the tongue and roof of mouth be so affected? What might be occuring here?

    MIght there be a anxiety response at play here?. During the day it is more noticeable when I get anxious. Perhaps a anxiety response is happening during sleep in response to obstructive breathing episodes? Is it the case that the body produces & secretes digestive acids when feeling anxious? But that I feel this primarily in my mouth -& not in my stomach, is key. (A associated sx during the day is occassional flushing of my face).

    Any thoughts on this? (My primary question is about the burning sensation on my tongue & roof of mouth that occurs most noticeably during sleep). What might you suggest by way of treatment? Does this sound like it is related to obstructive breathing sleep disorder? Perhaps it is really a anxiety/ digestive issue ?

    Most likely is all part of a inter-related syndrome! as you speak of in your book.

    ps – I use a lot of saline products – nasal gel, saline sprays, also use neti pot. Can all this saline be throwing off my ph balance?

  22. Steven Park on January 2nd, 2014 11:32 pm


    I can’t officially say without examining you in person, but larynopharyngeal relfux disease can happen without any stomach symptoms. Remember that it’s not just acid, but also bile, digestive enzymes, and bacteria that can go up into the mouth. You can stop breathing 25 times an hour and still not have obstructive sleep apnea, since you need at least 5 apneas per hour on a sleep study to have the diagnosis. Since an apnea or hypopnea must last for more than 10 seconds, having 25, 9-second breathing pauses will give you an official score of 0. This is called upper airway resistance syndrome and is treated the same way as obstructive sleep apnea (CPAP, dental appliances or surgery).

  23. Pascal on July 10th, 2014 3:46 pm

    Dear everybody,

    I m an interesting case. I had the operation with Linx, but I still have my symptoms of LPR (cough, lost of appetite, chemical taste in mouth).
    Could somebody say to me if you suffer also from a lost of appetite with LPR? My lost of appetite is strong in the morning and it becomes better during the day. Thanks

  24. Mike on July 28th, 2014 8:55 am

    Hi Dr. Park,

    What is your take on taking HCL w/ Pepsin as a supplement to help with reflux? I have read that LPR more often occurs when your digestive sytem is lacking in HCL.

  25. Red on August 12th, 2014 8:58 am

    Besides the numerous recommendations to reduce acid reflux, what can be done to eliminate the deposits of pepsin in the upper airway, larynx, ear, sinus, etc?

  26. Rosetta Johnston on December 8th, 2014 12:57 am

    I have been going round and round with one doctor after another. For more then four years I have have ever increasing asthma symptoms. In the beginning I was prescribed Advair which helped at first, but then I started having severe heartburn. Doctors said there was no connection, but at my insistence changed me to Dulera, when I started having blurry vision, and heartburn didn’t get better, either. Again, doctors said no connection; however, it is now listed as a known side effect. My research found as you say here, eating smaller meals etc. help, which they have, but still acid reflux doesn’t go away….

    When I read this report I felt like you were talking about me. I “can’t” sleep on my back, never have been able to. Post nasal drip, clearing my throat, hoarseness and only recently has a slight cough started. there are times when I have trouble swallowing, but that isn’t consistent.

    Here is my question. About the same time the asthma symptoms worsened I started snoring. I snore with my mouth shut which my husband finds amazing. I have tried to tell my doctors that I am sucking acid from my stomach and the only solution they have is medication. right now I am in a cycle being on predisone all the time, which I know isn’t good long term. I finish a dose and within two weeks I am wheezing again. I finished my latest round of predisone and Advair, abuterol inhalers and my nebulizer treatments barely relieve my symptoms….I feel like I am addicted to predisone! Would a dental appliance that would re-position my jaw help? It just seems if there is a vacuum effect there has to be a way to break the vacuum. Should I insisted on seeing an ENT. Could there be an issue with my sinus’ I did insist on a sleep study, but that said no sleep apena, but you said it still could still be an issue…….can you see how confused I am. I don’t want to take life long medication unless there is no other solution, at 62, all this is not good for my bones….HELP!

  27. Steven Park on December 8th, 2014 10:58 pm

    Ms. Johnston,

    Sorry to hear about your health issues. In general, you can keep going down the path of more and more aggressive treatment options for reflux. Unfortunately, they are likely to fail. What I see quite often is that repeated obstructed breathing that don’t last long enough to be apneas will still suction up your stomach juices into your throat. Even if you don’t have sleep apnea, it has to be treated like sleep apnea. Unfortunately, sleep physicians won’t treat you unless you have a sleep apnea diagnosis. However, CPAP and oral appliances can still be used. Good luck.

  28. Matthew Dickinson on January 29th, 2015 6:26 am

    I theorise that I have swollen nasal turbinates for two reasons. One is that OTC Oxymetazoline helps me temporarily when things like anti-allergy meds and Vics Vapour Rub do not. The other is that when I was tested for LPR reflux, a tube was put up my nose. When it was, my symptoms subsided for a whole 24 hours, and returned when the tube was removed. For the record, all reflux meds I’ve tried, including PPIs, Alkaline Water, Gaviscon Advance and even antidepressants have failed me.

    Swollen turbinates caused obstructed/unusual breathing. Unusual breathing causes some mild sleep apnae (I’ve woken up gasping a number of times) and can cause this vacuum effect both in the day and at night, leading to pepsin being detected. This is why I’m getting small amounts of reflux detected in my saliva, even though my dual-impedance studies say my reflux levels are normal, despite me binging on junk foods.

    Does that sound like a reasonable theory? Do you think if I treated my turbinate swelling, my reflux symptoms would stop?

  29. Bill on February 17th, 2015 5:42 pm

    Why is it so difficult to diagnose and treat Acid Reflux Symptoms? I too suffer albeit not has badly as some. I also have Sleep Apnea. I can’t get use to the CPAP. I used it last night and I awoke with severe heartburn. I haven’t had a severe episode in weeks. Ironically, I haven’t used the CPAP in weeks. So, I’m thinking my CPAP caused last night’s episode. I too am interested in the HCL with Pepsin. I am currently taking Lansoprazole DR 30 mg. I also started taking a probiotic. I’m thinking of seeing a Naturalist but I just don’t know what to believe and I don’t want to spend a ton of money. I just wish i could receive a more coordinated effort from my PCP. It just seems she wants to push the meds which would be fine if they worked.

    Any suggestions?

  30. Steven Park on February 19th, 2015 10:09 pm


    While CPAP helps millions of sleep apnea sufferers, sometimes, it can also cause more problems than it helps. And just because you’re using CPAP doesn’t mean that it’s working effectively. Treating reflux in general should help with sleep apnea, but it’s not always consistent. Unfortunately, PPIs like what you’re taking doesn’t treat reflux. It only lowers acid secretion.

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