Can Antibiotics Cause Heartburn?

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Do you have heartburn after taking antibiotics? You aren’t alone. It’s common for people to have heartburn when taking antibiotics.

Antibiotics are prescribed for treating bacterial infections. Unfortunately, antibiotics do not differentiate between good and bad bacteria. Good bacteria in our digestive system aid digestion and keep bad bacteria in check. When good bacteria are missing, digestive issues like heartburn occur.

Antibiotics contribute to heartburn symptoms and worsen gastroesophageal reflux disease (GERD) by eradicating good bacteria and by directly irritating the esophagus.

Common digestive side effects of antibiotics are:1

Antibiotics Heartburn Caused by Esophageal Irritation

Antibiotics are one of many caustic pills that cause esophagitis. The more caustic the antibiotic greater the risk of irritation.

What is esophagitis? Esophagitis is the inflammation of the esophagus, the tube that carries food from the mouth to the stomach. Common causes of esophagitis are acid reflux, medications, and infections affecting the esophagus. The irritation caused by esophagitis can be painful and make swallowing difficult.

Esophagitis is commonly caused by antibiotics accounting for close to half of all reported cases of pill-induced esophagitis. Doxycycline, tetracycline, and clindamycin are a few of many that make up a long list of antibiotics that cause esophagitis.

Causes of Antibiotic Pill Induced Esophagitis

Numerous issues can lead to esophagitis through extended contact with antibiotic pills.2

  • Antibiotic Causticity: The causticity of antibiotic pills can cause injury if pills remain in contact with the lining of the esophagus.
  • Posture: Poor posture can cause pills to get stuck in the esophagus.
  • Dry Mouth: Conditions or medication that lead to decreased amounts of saliva causing dry mouth can cause pills to get stuck in the esophagus when swallowed.
  • Number of Pills Swallowed: Taking a number of pills at the same time can cause them to get stuck in the esophagus.
  • Antibiotic Pill Size: Larger antibiotic pills can potentially get stuck when swallowed.
  • Lack of Water: Not drinking enough water when swallowing pills can cause them to get stuck in the esophagus.
  • Esophageal Motility Disorder: Esophageal motility disorders make swallowing both solids and liquids difficult.
  • Esophageal Strictures: Repeated exposure to refluxed acid in patients with GERD can form a ring of scar tissue called an esophageal stricture. Esophageal strictures make swallowing difficult allowing the prolonged contact of antibiotic pills with the lining of the esophagus.
  • Cardiomegaly: Cardiomegaly is the enlargement of the heart. When the left atrium is enlarged, it can compress the esophagus causing swallowing issues.
  • Age:
    ○ Elderly patients are more likely to develop pill-induced esophagitis. As we age, increased physical ailments require medications many of which are caustic or cause acid reflux by promoting the relaxation of the lower esophageal sphincter (LES). The LES is a ring of muscle at the base of the esophagus that needs to close tightly to prevent stomach acid from refluxing into the esophagus to cause heartburn.
    ○ The muscles weaken with age. This includes the muscle in the esophagus and LES. The weakening of these muscles can make swallowing pills more difficult and lead to the reflux of medication.
    ○ Stomach acid also decreases with age. Low stomach acid lengthens digestion time in the elderly. The longer antibiotics remain in the stomach the greater the risk of refluxing these caustic medications.

How to Avoid Antibiotic Pill-Induced Esophagitis

To avoid antibiotic pill-induced esophagitis, patients should:

  • Swallow pills when sitting upright or preferably while standing.
  • Swallow pills one at a time.
  • Swallow pills with 4 to 8 ounces of water.
  • Remain in an upright position for two hours after swallowing pills.
  • Ask your doctor or pharmacist if there is a liquid form of the antibiotic you’re prescribed.
  • Ask your doctor or pharmacist if the antibiotic pill can be crushed and mixed with water to make swallowing easier.
  • Ask your doctor or pharmacist if the antibiotic can be taken with food without limiting its effectiveness.
  • Ask your doctor if a less caustic antibiotic is available for treatment.
  • Ask your doctor if sublingual, intrarectal, subcutaneous, or intravenous, forms of antibiotics are available for treatment.
  • The elderly should increase stomach acid to improve the digestion time of antibiotics.
  • The mucosal membrane lining the esophagus and stomach can be bolstered with mucilage for added protection against esophagitis. Mucilage is a substance produced by plants and is found in aloe vera, licorice (use DGL form), slippery elm, and marshmallow root.

Patients who are at risk of a recurrence of antibiotic pill-induced esophagitis or the development of chronic esophagitis from taking antibiotic pills are those who have esophageal issues that restrict swallowing, the elderly, those whose health condition prohibits swallowing pills with an adequate amount of water, and those who are unable to sit up.

Related Content:

Antibiotics Heartburn Caused by the Loss of Good Gut Bacteria

Antibiotics are used to kill off bad bacteria that are causing illness, but they also kill off good bacteria in the digestive system. These good bacteria aid the digestive process. When good bacteria are missing, we can suffer from digestive issues like acid reflux and heartburn.

How Good Gut Bacteria Loss from Antibiotic Use Causes Heartburn

How can the lack of good bacteria from the use of antibiotics lead to acid reflux symptoms like heartburn? When good bacteria in the digestive system are killed by antibiotics, an overgrowth of bad bacteria can lead to excessive gas, bloating, belching, reduced stomach acid, and constipation. All of which can lead to heartburn.

Antibiotics Heartburn from Gas and Bloating

Bad bacteria produce hydrogen and methane gas causing an increase in abdominal pressure.

This increase in abdominal pressure will weaken the lower esophageal sphincter (LES) prohibiting it from closing tightly enough to keep stomach acid from refluxing into the esophagus. The LES is a ring of muscle at the base of the esophagus that opens as food travels to the stomach and closes to keep acid reflux from occurring.

The gas produced by bad bacteria not only causes abdominal pressure. It can lead to belching. Belching will help lower abdominal pressure, but it can also force stomach acid through the LES into the esophagus.

Antibiotics Heartburn from Reduced Stomach Acid

An overgrowth of bad bacteria in the digestive system will cause a reduction in stomach acid. This initially sounds great to those suffering from acid reflux symptoms like heartburn, however, stomach acid actually triggers the LES to close. If the LES doesn’t close tightly enough, acid reflux can occur.

For many people, heartburn isn’t from too much acid. It’s a lack of acid. Our stomachs are designed to handle stomach acid. The stomach has a lining that protects against it. The problem is when acid refluxes into the esophagus. The lining of the esophagus doesn’t have the same protective lining as the stomach.

Acid Reflux After Antibiotics Due to Constipation

Antibiotics not only cause heartburn during their use but can also lead to heartburn after use.

Diarrhea may be experienced during the use of antibiotics but constipation can be experienced after the discontinuation of antibiotics.

Why does constipation occur after discontinuing antibiotics?

Without good bacteria to keep the bad bacteria under control, bad bacteria will impair the digestive process causing it to slow by preventing the synthesis of digestive enzymes needed to break down proteins into amino acids and the absorption of nutrients.

The increase in abdominal pressure due to constipation can prevent the LES from closing properly leading to acid reflux and heartburn.

How to Treat Heartburn from Antibiotics with Probiotics

Probiotics are good bacteria that need to be ingested to rebalance gut bacteria after discontinuation of antibiotics. The reintroduction of these good bacteria will improve digestive function and reduce acid reflux symptoms like heartburn.

The use of probiotics during antibiotic treatment may help restore stomach acid and alleviate gas, bloating, and belching even though antibiotics will continue to kill these good bacteria.

Probiotics rebalance digestive function after antibiotic use and thus reduce the instance of heartburn by:

  • Preventing the overgrowth of bad bacteria which produce gas leading to bloating and belching.
  • Preventing constipation by eliminating bad bacteria that cause slow, inefficient digestion.
  • Promoting optimal stomach acid levels. Stomach acid helps the LES close properly, kills harmful bacteria, improves absorption of nutrients, and reduces the instance of constipation.
  • Improving food and nutrient absorption by helping break down food for easier digestion thus reducing the possibility of constipation. Improved nutrient absorption also provides the digestive system with needed nutrients for proper function.
  • Maintaining muscle activity which moves material through the digestive tract.
  • Preventing leaky gut and helping with antibody production which boosts the immune system. A healthy immune system also helps protect against bad bacteria overgrowth.

Fermented foods and probiotic supplements can be used to reintroduce good bacteria into the digestive system after the use of antibiotics. Fermented foods and beverages like buttermilk, kefir, kimchee, kombucha, miso, sauerkraut, sour cream, and yogurt are the best sources of probiotics, but avoid pasteurized versions of these. Good bacteria are killed off in the pasteurization process. Consume probiotic foods that are unpasteurized.

Though cultured dairy products are great sources of probiotics, avoid these when first reintroducing probiotics and when you have heartburn. Dairy products contain lactose, a sugar on which the bad bacteria will feed. Dairy products can also increase heartburn symptoms. Initially, dairy products can make heartburn feel better, but they will prompt the stomach to produce more acid for breaking down calcium, fat, and protein found in these foods. The additional acid can cause heartburn symptoms to rebound.

If you can’t find unpasteurized, probiotic foods, you can always make your own at home. Lacto-fermented foods are quite simple to make.

Good Bacteria Must Be Fed

Good bacteria or probiotics need a food source called prebiotics. Prebiotics are nondigestible carbohydrates found in foods like barley, oats, flax, wheat, beets, carrots, garlic, leeks, legumes, onion, artichokes, asparagus, and radishes. They can also be found as prebiotic supplements.

Avoid or keep sugar, processed foods, animal fats, and animal protein to a minimum. These food promote bad bacteria growth.

9 Things to Remember When Taking Antibiotics:

  1. Don’t take antibiotics unless they are really needed. Too many people abuse antibiotics.
  2. Antibiotics will likely cause heartburn.
  3. Mucosal supplementation in the form of mucilage (aloe vera, licorice (use DGL form), slippery elm, and marshmallow root) is available for protecting the lining of the esophagus and stomach from the causticity of antibiotic medications.
  4. Take pills while in an upright position, with 4 to 8 ounces of water, and remain upright for 2 or more hours.
  5. Taking antibiotics with food may reduce stomach irritation.
  6. Antibiotics kill off needed good bacteria in the digestive system.
  7. Rebuilding good bacteria after getting off antibiotics is essential for digestive health.
  8. The general tips for avoiding heartburn can help during antibiotic use.
  9. Heartburn medicine can affect the absorption and effectiveness of some medications. Speak with your doctor before taking acid reducers for heartburn symptoms.
Man taking antibiotic pill with a glass of water. The graphic asks... Why do antibiotics cause heartburn?


1) “Side effects – Antibiotics.” National Health Service, UK, September 6, 2016.

2) J. Walter Kikendall, MD. “Pill-Induced Esophagitis.” National Center for Biotechnology Information, U.S. National Library of Medicine, Gastroenterol Hepatol (NY), April 2007

38 Replies to “Can Antibiotics Cause Heartburn?”

  1. I already have GERD, successfully managed by nexium/Zantac treatment for years. Recently started taking doxycycline/rifampin combo for staph, along with probiotic, and started developing bad heartburn after about 4 days. Stopped both meds 2 days ago, still have heartburn even with my GERD meds. How long will this last after stopping meds? Thank you.

  2. Hello i have taken a clindamycin for a few days now i have found out 2 or 3days ago the feeling of burning sensation on my chest is this what they call acid reflux or heartburn my Dentist give this antibiotic for my tooth extraction 2 days from now aside from clindamycin i take mefenamic acid for pain and metrolpolol neobloc for my BP im afraid if this continue will acid reflux or heartburn destroy my esophagus and i feel right now when i swallow i feel a little irritation when food goes down.

  3. Hello Steve
    My doctor told me that I have tuberculosis after x-ray ct scan and biopsy test. He prescribed tuberculosis antibiotic to treat the bacteria. Since I started I feel very bad heartburn, vomiting, nausea, and also loss of appetite. After two months doctor told me again that the antibiotic doesn’t work very well also he said your body doesn’t respond to this antibiotic. So my question is what caused for that Or is there any antibiotic for tuberculosis. Many thnx

    1. Hello Hamse, the majority of TB cases are cured with the right medication and when it’s taken correctly. You’ll have to work with your doctor to find the right medication. Antibiotics usually have to be taken for extended periods of time to fight off the infection. From your experience with your previous antibiotic, you’ll probably continue to have acid reflux symptoms like heartburn, vomiting, nausea, and loss of appetite until your good gut bacteria can be restored.

  4. Can IV antibiotics cause heartburn? My husband is getting IV antibiotics for cellulitis and has constant heartburn.

    1. Yes, IV antibiotics can cause heartburn. Both oral and IV antibiotics can eliminate good bacteria in the digestive tract which will lead to acid reflux and heartburn. Hope your husband is better very soon!

  5. I am taking antibiotics to treat SIBO(Small intestinal bacterial overgrow) and now I am having horrible heartburn/acid reflux. I heard that probiotics can make sibo worse, do you have any suggestions?

    1. Hello Maria, if your medical professionals are telling you to stay away from probiotics until your SIBO has been eliminated, you should follow their direction. If you have not, please read our article on SIBO. I mention mucilage at the end of the article. Mucilage like DGL and slippery elm will help reduce heartburn by coating and protecting the esophagus. For nighttime relief, acid reflux pillows like the Medcline Reflux Relief System are very helpful.

  6. Hi,

    I finished a couple days on Cipro 500mg and now have stopped by suddenly have acid reflux. Is it better to take a probiotic supplement or just eat yogurt?

    1. Hey Dave, I’d say both. You want to try to build up a variety of good bacteria. Make sure you’re eating yogurt that’s not been pasteurized. Pasteurized yogurt is devoid of probiotics and has sugars that will feed bad bacteria. You might take a look at our post on lacto-fermented foods for treating heartburn.

      1. I have an acid reflux or i dont know maybe hurt burn after taking a clindamycin for a few days cause i’ve been scheduled by my dentist 2 days from now for a tooth exrraction should i stop the medication,im afraid it will destroy my esophagus and when i swallow a liitle bet pain….

  7. Am currently taking Clindamycin following oral surgery and twice have had horrible heartburn immediately following a dose (4x daily/150mg). I eat one carton of yogurt mid-morning and take an acidophilus tablet each afternoon with a snack. Tonight’s dose of antibiotic triggered heartburn again and I just tried a half tablespoon of apple cider vinegar in 3 ounces of apple juice. So far, no relief, which is surprising since this always works for me. Will try sour cream next or it will be a LONG night. Thank you for a well-written, informative article.

    1. Hello Veritas, Clindamycin is an antibiotic that can irritate the esophagus. In this case, a mucilage to coat and protect the esophageal lining might be better than apple cider vinegar. I like DGL licorice and slippery elm lozenges. You might ask your pharmacist to see what they think. Hope you’re feeling better soon!

  8. I had 2 rounds of amoxicillin 500mg 3 times a day and shot of rocephin with steroids. The day after i finished the antibiotics my acid reflux got so bad my throat constantly burns can’t lay down to sleep and my nose burns also. No antacid is touching it. I took zantac which just takes the edge off so i can sleep some. Do you think antibiotics did this to me it did not happen till i took them and its been bad ever since. I have been off antibiotics for 1 week now and i been eating yogurt and drinking butter milk also eating healthy but not better yet.

    1. Hello Misty! Antibiotics can cause your symptoms and it can take time for your digestive tract to repopulate good bacteria. Most groceries sell yogurt and buttermilk that has been pasteurized. This kills off the good bacteria that you’re trying to replace. The sugars including lactose can actually feed the bad bacteria in your digestive tract. You might check out our post on Lacto-Fermented Foods and Beverages Treat Heartburn. Acid reflux pillow systems and sleep positions can help relieve symptoms when you sleep. Hope you get to feeling better soon!

  9. Hi
    Could I have your opinion please. suffered from reflux and constipation for a long time. Last year I was on IV meds for 20weeks. Imipenem,tigecycline, Amikacin. My reflux constipation is worse since the treatment. Doctors say they can’t find anything wrong. Could it be caused or I rated by the IV meds.
    Look forward to hearing from you.

    1. Hello Lea, antibiotics kill off healthy gut bacteria. This can cause reflux and constipation. It’s important to restore healthy gut bacteria after taking antibiotics by eating probiotic-rich foods or supplements. Talk to you doctors about how gut flora changes when taking antibiotics and check out the articles on probiotics, fermented foods, and Candida. Best wishes!

  10. Hi, I was onnly on trimethoprim antibiotics for 3 days for a water infection. On the 3rd day, I had acid reflux and bad belly pain. Been off the tablet for 14 days now. Still in pain. How long does it take to settle down? It’s unbelievable what antibiotics can do to you.

    1. Hello Bianca. Unfortunately, there isn’t a set number of days for digestive recovery from antibiotic use. Individuals recover at different rates. Acid reflux and stomach pains are common side effects of antibiotic use. Be sure to replenish the good bacteria (probiotics) killed off by the antibiotics and avoid heartburn trigger foods during this recovery period. Follow all other directions from your physician and if you have further concerns, your physician should be able to address them. Wishing you the best in your recovery process!

  11. Hi, can someone please help me. I’ve been taking erythromycin to treat acne, now I’ve got acid reflux. Constant source taste in mouth. Feel like I’m going to choke.

  12. Last week blood work showed I have a severe bacterial infection compounded by Salmonella poisoning. I am on a very aggressive course of antibiotics, 4 pills in the morning and 4 pills at night. Yuck! I wake up with the most horrible taste in my mouth and I know it is acid reflux. The antibiotics are wreaking havoc on my system. I am unclear as to whether or not it is safe to continue taking my probiotics while on antibiotics. Opinions?

    1. Hello Judy, taking probiotics during and after antibiotic treatment is important. Yes, the antibiotics will work to kill off the good bacteria introduced through probiotic supplements but these good bacteria are important for digestive health. Taking probiotics while on antibiotics can help slow the growth of bad bacteria and may also reduce the side effects of some antibiotics. Wishing you a speedy recovery!

  13. Hi Steve
    I live in Africa
    I have been in a course of antibiotics 14 days (Levofloxacin)
    It caused me constipation and digestive problems
    I took a lot of natural probiotics like yogurt and pickles
    I drank licorice
    Everything became good after omeprazole, except for belching and heartburn
    Do you have any advice for me ??
    How long is healing?

    1. Hello Lucas, hope all is better now. The time for healing the gut after taking antibiotics is different for everyone. Your doctor knows your condition and could provide you a better answer. Continue eating nonpasteurized probiotic food to replenish the good bacteria in your digestive tract. Probiotic supplements are also an option. Licorice, marshmallow root, and slippery elm can help coat your esophagus and lower heartburn symptoms. Best!

  14. I have and still am on antibiotics first for a UTI now for infected leg ulcer how can I replace my body with some good bacteria

    1. Hello Linda! How to Treat Heartburn has an article, “Probiotics for Heartburn Relief” that discusses how to introduce probiotics into the digestive system. The section “Taking Probiotics for Heartburn Relief” is where your answer is specifically discussed. The best source of probiotics will be found in unpasteurized fermented foods and beverages. Probiotic supplements are also available. Wishing you a quick recovery!

  15. Well. Been taking antibiotic “Amoxicilin” for 4 days now for a possible throat infection and now I woke up with the feeling of having a wet sponge stuck in my chest and upper throat when i swallow. I feel the need to burp. ANTIBIOTICS SUCK! Great article.

  16. I never have had heart burn like this in my life . My stomach hurt and was upset all day long and it would wake me up at night. Ceftin was horrible and it had been 7 days since my last dose of the ten prescribed.
    LIKE MAGIC after I ate five yogurts yesterday my heart burn was gone!!!

    Thank you for posting reliable information on line.

  17. But how would one be comfortable sleeping on your left side on a wedge pillow? Please advise.

  18. Put me on the 2 week course of antibiotics, which eradicated it. Ever since then I suffer daily from GERD, which is how I ran into your article, I know link my condition to the fact of taking antibiotics, which kill certain types of bacteria including H. Pylori, and causing overgrowth of other bacteria with all leading consequences.

  19. Thank you for the advice on sleeping on the left side . I find first thing when I wake up I feel worse so i shall definitely give that a go.

    1. You are welcome, Carol. Thank you for reading. You might also try sleeping on a wedge pillow to reduce pressure on the LES and lower chances of acid reflux. Best!

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