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Trouble Digesting Breast Milk? How to Remedy Infant Acid Reflux

If your newborn infant is not properly digesting breast milk, your doctor may suggest that you feed your baby formula. In extreme cases, a doctor will recommend an infant dose of prescription antacids.

Is an infant-sized dose of an antacid really the answer?

Infant acid reflux occurs in about half of all babies during the first three months after birth. As common as infant acid reflux is, it is a condition that tends to resolve itself as the baby grows - usually between 9 and 12 months old.

In some babies, the valve that separates the esophagus from the stomach is weak and still gaining muscular tone. This valve is called the lower esophageal sphincter.

Infant acid reflux occurs in almost 50% of babies under three months old. Instead of turning to prescription antacids to correct the issue, you can improve your baby’s digestion by balancing his inner ecosystem first of all.

When breast milk enters the stomach, the lower esophageal sphincter contracts. This contraction prevents both food and stomach acid from rising up into the esophagus. When the sphincter fails to fully close, stomach acid and partially digested breast milk reflux back up into the esophagus. This irritates the esophageal lining and causes pain.

When a baby or newborn has acid reflux, breast milk goes undigested.

For new parents, infant acid reflux can be alarming. A baby may cry more than usual, sometimes for hours at a time. And parents may worry that their baby is not getting all the necessary nutrients.

Formula, which doctors will often recommend, may seem like a suitable alternative to breast milk. Especially when recommend by your pediatrician. However, there are many benefits to breastfeeding your baby that formula does not offer:

  • Breast milk encourages the naturally permeable lining of an infant’s gut to heal.
  • Breast milk inoculates the baby’s digestive tract with beneficial bacteria.
  • Breast milk educates the baby’s immune system. 
Make sure that both the baby and the baby’s inner ecosystem are well nourished.

One way to nourish a baby’s inner ecosystem is to place a few drops of cultured vegetable juice on your baby’s tongue.

The juice from a batch of lacto-fermented veggies is full of beneficial microorganisms that immediately begin to improve digestion. Improving digestion means that your baby is receiving maximum nutrient value.

It is important to find a fermented vegetable or sauerkraut from a source that you trust or to make your own with the Culture Starter. Store-bought brands can be poor in quality.

While your baby’s digestion improves, you can also place a small amount of organic, grass-fed ghee on your baby’s tongue.

In India, ghee is revered as a sacred food that cultivates life force. Made from butter, ghee is filtered and clarified. The proteins typically present in butter are removed. This makes ghee uncommonly safe for those who have sensitivity to dairy. In India, ghee is considered an essential digestive tonic.

According to ancient Indian tradition, newborns are immediately given a small pat of ghee to suck on. (1) This practice, which is still carried out today, is said to improve the digestion and assimilation of nutrients. Ghee also promotes healthy elimination. (2)

In addition to strengthening digestion, ghee is full of important fatty acids that sustain energy and fuel the development of brain function. More than 50% of the nutrients in breast milk are in the form of fats. Fat satisfies a baby so that it can sleep soundly through the night.

Consider, too, a tongue-tie.

Sometimes a baby’s inability to feed has to do with a little piece of skin that unites the baby’s tongue to the floor of the mouth.

A tongue-tie, also called anklyoglossia, results in an infant being unable to fully latch onto a mother’s breast.

Signs of a tongue-tie are:

  • Colic
  • Acid Reflux or GERD
  • Clicking sounds while breastfeeding
  • Poor weight gain and failure to thrive
  • Irritability during and after breastfeeding

In extreme cases, a tongue-tied infant will be placed on formula, given medications, screened for Crohn’s disease, and even given a barium swallow test - often before a tongue-tie is ever considered.

According to pediatric dentist Lawrence Kotlow, babies that express colic or reflux symptoms should first have an oral exam. If there is a tongue-tie, switching over to formula or putting an infant on prescription medications will do little to correct the problem or improve an infant’s ability to thrive. (3)

Keep in mind that prescription reflux medications have not been fully studied.

This is true for both infants and adults. In a baby, prescription antacids can actually lead to a decline in overall health. (4)(5)

Because antacid medications reduce the highly acid environment of the stomach, this can actually make the body more susceptible to gut infections.

This is bad news for a colicky baby that is put on antacids: an infant’s gut is naturally permeable at birth and can sometimes take several months to fully seal.

Just recently, the FDA announced that prescription antacids could promote infection of Clostridium difficile bacteria. (6) An infection of C. difficile, which causes diarrhea, is especially dangerous for infants because they are sensitive to water loss.

What to Remember Most About This Article:

Conventional methods to remedy infant acid reflux, such as switching to formula or using prescription antacids, do not solve the underlying cause of the symptoms. What can be done?

  • You can safely and effectively nourish your baby with small pats of grass-fed ghee.
  • Giving your infant a dropper-sized dose of fermented kefir or the liquid from a batch of cultured vegetables encourages a healthy inner ecosystem. This is absolutely necessary in order to fully break down the nutrients in breast milk.
  • Check for a tongue-tie. Fussiness during breastfeeding or signs of acid reflux may have to do with a baby’s inability to properly feed.
  • Unless you make your own formula at home with nourishing ingredients, infant formula can permanently and negatively influence the microflora of your baby’s intestinal tract.
  • Prescription antacids are designed to make the environment of the stomach less acidic. In both adults and babies, this opens the body up to a gut infection since the stomach’s acidity is one of the body’s first lines of defense. 

Product Recommendations:

  • Kefir Starter

    Kefir Starter

    Better Digestion, Boost Immunity

    Kefir has many benefits, including better digestion of fats, proteins and carbohydrates. It has been known for thousands of years for its anti-aging and immune-enhancing properties.

    Kefir is an ancient cultured food, rich in amino acids, enzymes, calcium, magnesium, phosphorus and B vitamins. Kefir means "feel good" in Turkish, and that's just how you'll feel after drinking a glass in the morning! Easy and fun to make at home, it is superior to commercial yogurt. An absolute must after antibiotic use!

    Unlike yogurt, kefir can actually colonize the intestinal tract and is simple and fun to make at home. To make kefir: Mix one packet with 1 quart of warm milk, cover and set at room temperature for 18-24 hours. Refrigerate and enjoy!

    Each packet yields 1 quart of kefir, and can be reused up to 7 times. This means you can create 10 ½ gallons of kefir from one box!

    • Digest fats, proteins and carbohydrates
    • Has anti-aging and immune-enhancing properties
    • Rich in amino acids, enzymes, calcium, magnesium, phosphorus and B vitamins
    • An absolute must after antibiotic use
  • Veggie Culture Starter

    Veggie Culture Starter

    Resist Infections, Enhance Digestion

    • Ideal for appetite and weight control
    • Ideal for pregnant women
    • Ideal for children with Autism and ADD
    • Can be enjoyed daily
    • Easy to make at home


  1. Laroia N, Sharma D. The religious and cultural bases for breastfeeding practices among the Hindus. Breastfeed Med. 2006;1:94-98.
  2. Kathleen M. McKenna, et al. Practice of Prelacteal Feeding to Newborns Among Hindu and Muslim Families: Prelacteal Feeding Among Hindu Families. J Midwifery Womens Health. 2009;54(1):78-81.
  3. Kotlow, Lawrence. Infant Reflux and Aerophagia Associated with the Maxillary Lip-tie and Ankyloglossia (Tongue-tie). Clinical Lactation. 2011; 2-4; 25 - 29.
  4. JJ Baudon. [Gastroesophageal reflux in infants: myths and realities]. Arch Pediatr. 2009 May; 16 (5): 468 – 473.
  5. Y. Vandenplas, et al. The diagnosis and management of gastro-oesophageal reflux in infants. Early Hum Dev. 2005 Dec; 81 (12): 1011 – 1024.
  6. U.S. Department of Health and Human Services: U.S. Food and Drug Administration. FDA Drug Safety Communication: Clostridium difficile-associated diarrhea can be associated with stomach acid drugs known as proton pump inhibitors (PPIs).

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  • Vachhani

    reflux is due to acid. How tounge tie can be the reason of reflex if baby is sucking enough milk? Please explain more.

  • Laura

    How does tongue tie have anything to do with how well they digest the milk??? Doesn't it just make it difficult to get the milk out? Once it's out it's the same milk! Also, 6 out of 8 of my babies spit up but it never seemed to cause the colic. They have no expression or they might even be smiling when they do it. I've had colicky babies but it seemed totally unrelated to their screaming times. One of the most colicky didn't spit up.

  • Jenni

    My son was diagnosed with reflux. We tried just taking out dairy and other foods that might irritate him (as the lactation consultant suggested) but, it only helped a little. The doctor suggested a small dose of antacid and it was a lifesaver. He was a completely different baby. As he got older we were able to go without the antacid and just do no dairy for me. Now, at 7.5 months I can have dairy again and he is off the antacids completely. My doctor never suggested formula as help for reflux.
    My youngest brother had problems with breast milk AND formula due to a carbohydrate intolerance. (I think?) He had to be hospitalized for, I know that in very rare cases breast milk can't be digested by kiddos (of course this was 20+ years ago so maybe the information has changed.) But, from my experience with my son I've found that just changing my diet helped after a few days!
    @Salwaty— I was able to eat goat and sheep cheese with no reaction to my son. I drink rice or coconut milk.

  • Brian

    People can be so opinionated... Wow.

  • Salwaty

    Oh gosh. My son is 6 weeks old and was diagnosed with acid reflux. He is on losec 10 mg a day and my breast-feeding only. It's is exhausting to feed on demand as the doc recommended . I am exhausted physically and my nipples crack at times and sore! I have been watching my diet no meat. No sweets. No junk foods. No juices I guess need to stop diary though I'm not a milk lover! Wanted to supplement but using goat milk formula. Anyone with any experience on goat milk and infants? Help!

  • Millie

    As an RD, I would always recommend to contact a lactation consultant (IBCLC) and La Leche. Sometimes La Leche or lactation consultant is aware of other things due to their high level of experience. I would want to ask the person whose baby was not able to digest the milk if they were on a PPI at the time. My niece's baby developed an allergy to her breast milk due to not being able to digest the protein. AFTER they started the PPI. I think a mix of Donna's suggestions along with the suggestions of the lactation consultant and La Leche would be the best. Sometimes it is also an imbalance of foremilk and hindmilk. Just because mom's milk is natural, doesn't mean that sometimes something doesn't go wrong with her milk. Mom should also be taking probiotics from cultured foods which helps with her milk.

  • Brian

    I have to say, this tactic truly solved the GI distress in my newborn son (now 10 months old and using probiotic therapy daily). GERD was a major problem for him at the start, and when his pediatrician recommended drug therapy, namely H-2 receptor antagonists and/or PPIs, I felt the need to do some further homework.

    As a pharmacy student, I know all too well the rampant effects delivered by such medications. And, as far as PPIs are concerned, why would I ever feel comfortable giving my newborn baby a drug that impairs his natural use/need for gastric acid supply? In my opinion, PPIs are a terrible drug of choice in all populations, child or adult...but that is irrelevant here. Babies do not need western medication unless they've a true defect or life-threatening condition; GI distress, caused by immature and under-developed tissue, is not's natural.

    Since I use probiotics daily--and so many baby formulas contain prebiotics for floral development-- and with great results re: generalized wellbeing, it seemed obvious to me that this would gradually help his pain and inability to digest the macromolecules responsible for his discomfort (without inhibiting his own innate ability to function correctly).

    Finally, in response to Diane's comment...I want to agree with you. But 3 physicians in my son's PCP group all shared the view that the proteins in my wife's milk truly were upsetting his stomach. Once he shifted to a formula with broken-down proteins, his issue was improved. We tried breast milk again 2 months later and re-encountered the same initial problem. As for her diet, it is caffeine-free, gluten free, processed sugar-free, high in vegetables/good fat, with a moderate (though not by any means excessive) level of protein. It truly devastated my wife not to be able to feed naturally...

  • Wendy

    I have been doing a modified version of the BED for years--no dairy, gluten, chocolate, or fruit etc. My baby still has trouble with breastmilk. I've decided to go to stage 1 of BED again. This is very helpful. Thank you for giving me some ideas.

  • diane

    I do not agree with this article. It does not address the number one reason for a colicky, breast fed baby; what the mother is eating. Dairy, chocolate,& strawberries are just a few of the foods that babies can not tolerate. This happened to me. I cut dairy from my diet and the colic immediately stopped. Also, a breast fed baby with reflux is most often not an acid reflux issue. The J shape in in the esophagus sometimes is not fully developed yet and is still in a straight position. This allows for the milk to come right back up. This situation will mature on its own. Switching to formula is ludicrous. Again, the mother should eliminate from her diet the high allergy foods. There is nothing better than breast milk for the digestion of the baby with the mother watching what she is eating. I recommend all mothers who are breast feeding contact the La Leche League, a well established support for women who are breast feeding. If your doctor suggests that you switch to formula, you have the wrong doctor. This article is just trying to sell products.

  • Kyle A Knisely

    As a board certified Lactation Consultant I have to say I am pulling my hair out screaming at the ridiculousness of this article. There is no such thing as a baby not being able to digest breast milk..NONE. Though the mother may be eating some unnatural food that is passing into the breast milk and the babies internal wisdom is saying ...stop that. In my practice 9.9 times out of 10 the culprit is know, milk designed by God for COWS!!!! And most importantly you failed to recommend that this mother get herself to a lactation consultant for an evaluation...never would tongue tied be a complication for not digesting well. Where in heavens name did you get your information??? PLEASE consult with an IBCLC before embarrassing your good name and all the other important information you have for adults!!!

  • Sabrina

    Thanks for bringing this topic up. It is very imprtant and a lot of parents do not have accurate information or alternatives to the too often perscribed routine of stop breastfeeding and give formula protocol givven by a lot of pediatricians. I want ot mention, tongue tie can be very hard to diagnose if it is posterior or ssubmucosal. Definatly have a professional who is well versed in tongue tie examine the baby like an IBCLC or other professional in your area such as Dr. Kotlow. When treating a baby for acid reflux, it is also important to look at the mother's gut function. It can have an impact on the baby's system as well.

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