Reflux, medication and your baby’s sleep

Reflux, medication and your baby’s sleep

Reflux, medication and your baby’s sleep

If you’ve been in the parenting game for more than 5 minutes, chances are you know someone who’s baby has reflux, and probably someone who has had to have medication for their baby’s reflux.

Reflux diagnosis has increased so much that one NZ study ( Blank M. L et al. 2017) showed an increase from 2.4% of babies being prescribed a PPI, to 5.2% in just 7 years (2012). In fact these numbers peaked in Canterbury in 2009 where 10% of all babies born that year were prescribed a PPI as a newborn! 

This article is not to dismiss anyone’s experience of reflux or tell you not to medicate your baby. I am simply looking at a recent (2022) comprehensive overview of the mechanism of actions, use (and misuse) in infants and the safety of PPIs.

The science of proton pump inhibitors (PPI’s)

A PPI is a proton pump inhibitor, you might know them in NZ and Australia as Losec or omeprazole. These drugs are among the most prescribed drugs worldwide. They are approved for use in children over 1 year old but are very commonly prescribed for infants suffering from reflux (GERD) or colic symptoms. A PPI effectively blocks the proton pump H+-K+-ATPase found in the parietal cells in the stomach, preventing the enzyme from triggering the release of stomach acid. No stomach acid = no pain from vomiting.

Side effects?

If you talk to enough parents who have had a baby prescribed omeprazole, for every parent who tells you it was life saving for their baby and changed them into a happy feeding content baby, you hear concerns from another parent that they feel like it makes their baby’s symptoms worse.

Baby starts to cry more, fuss more, feed less, struggle with wind and can be generally not happy. But these concerns are often dismissed by the person who prescribed the drug, or the parents feel it’s something they need to push through for weeks and weeks.

The tricky thing is, the common side effects (1 in 100) of omeprazole include headache, nausea, stomach pain, constipation, excess wind, vomiting, and diarrhoea. This is a daunting list, and none of these things your baby can communicate to you in any way except via excessive crying!

But we might think they’re crying due to the reflux… and push on with the drugs, or ask for the dose to be doubled to be more effective…

Is it reflux or is it the PPI?

The concern with this approach is shown in Hussain et al 2014, where doctors did a comprehensive study with 344 infants who were having troubles with reflux, and gave 1 group 5mg of a PPI, one group 10mg of a PPI and one group a placebo.

The study went on for five weeks, all three groups showed clinical improvements and parents reported improvements. Yet when you look closely, the only common denominator in all 3 groups? Time!

The babies aged 5 weeks during the study, and we know that a lot of reflux is physiological and improves as baby’s age. It’s most often resolved by 6-12 months.

What are the options or alternatives?

Currently the guidelines for babies showing symptoms of reflux or GERD are in this order. (Dipasquale et al. 2022)

  1. Thickening formulas or feeds, discussing effective winding, and avoiding over feeding which is easy to do when baby cries a LOT!
  2. Trialling allergy elimination especially cows milk as there is a strong link between CMPA (Cows milk protein allergy) and reflux or GERD. (Roden et al., 2018)
  3. Trial of PPI (omeprazole, losec) to be considered after referral to a pediatric gastroenterologist after the failure of the first- and second-line treatments listed above.

But how many times are the first- and second-line treatments skipped or not even suggested? I’m not anti PPI’s or pro alternative treatments, but I am pro all options being explored and best practice being followed for all babies.


The 4th option is Probiotics

If you’ve read my article on colic, you’ll know the wonders of probiotics to treat excessive crying in infants.  One such study looked at the effectiveness of Lactobacillus reuteri DSM 17938 for 90 days in 589 term new-borns aged 1-11 weeks.

Vomiting and spilling was measured as a primary outcome of this study and at the end of this 90 day trial there was a statistically significant difference between the placebo group and the probiotic group. The probiotic helped with reflux symptoms! There was also a huge improvement in crying time per day which we all know is a big stressor with babies with colic or reflux.  

Furthermore, since 2018 it’s been best practice to prescribe probiotics in conjunction with PPI’s as we know the long term administration of drugs like losec can change the gut bacteria population as these drugs change the pH of the gut. (Belei et al. 2018)  

A study by Dr Belei looked at infants been given PPI’s with and without the wonder probiotic Lactobacillus reuteri DSM 17938. After 12 weeks of treatment, an imbalance of gut bacteria was detected among 56.2% of children from placebo group compared to 6.2% of children from the probiotics group. That’s a remarkable difference!

You might think…. Really, what does it matter if the gut bacteria are a bit out of whack?

You’re right that the symptoms of this could be asymptomatic, or they can include bloating, abdominal pain, diarrhoea, steatorrhea, excess wind, dyspepsia, nutrient malabsorption, weight loss, and failure to thrive. All of these can lead parents to see a baby in pain and crying, and uncomfortable, questioning if their reflux medication dose needs to be doubled again…

We’ve known this since 2018 but how many babies do you know being given losec or omeprazole without a probiotic?

What about sleep?

If you’ve got a fussy baby, a crying baby, an uncomfortable baby, a baby with these symptoms and with or without a diagnosis of reflux or GERD you are likely struggling with sleep, and this is likely compounding your baby’s symptoms!

As we tire our pain tolerance lowers, and this is true for babies too. What might be a little discomfort becomes a big pain as they get tired.

Tired signs in new-borns include crying, fussing, and less commonly known spilling or vomiting. As your new-born gets closer to their max awake time, you’ll likely notice their symptoms of reflux and colic get worse. You’ll want to avoid over tiredness like the plague, keep a strict eye on the clock, and your baby’s tired signs.

But how do I get my fussy, refluxy, crying baby to sleep you say!

We know that left side positioning of babies decreases spilling and vomiting episodes, so if you are holding your baby getting ready for a sleep, try either left lying across your front cradle hold or upright over your shoulder. Always have baby sleep on their back, but left positioning is great for settling in your arms or in their cot as you pat or rub their back to settle (rub if patting makes any spilling worse!). Roll them once they’ve settled, and always supervise any left laying time.

Try to keep any top up feeds away from naps, give your baby the 20-40 minutes for gastric emptying before trying to settle to sleep for a nap.

Dummies/pacifiers work wonders in newborns with and without reflux! If you have a spilly baby offering a pacifier will not only ease any discomfort without over feeding, but it will also help trigger baby’s calming reflex and make sleep come easily. Even if your baby doesn’t sleep with a dummy, offering one to a reflux baby in their wind down time can aid in calming and wind for a reflux baby.

Swaddling your fussy new-born will also likely help with any reflux symptoms but watch how tight your wrap/swaddle is over their tummy. Too tight and you’ll make things worse, consider something with a bit of give like an ergo pouch zip up swaddle, or a love to dream.

Establishing a bit of a daily routine with your reflux baby will also aid in sleep and symptoms. Having regular sleep times allows your new-born to start to predict and know when sleep is coming, and thus sleep is easier! Having somewhat regular feed times will help you avoid over feeding, and confusing crying due to tiredness with crying due to pain or hunger.

Just like with colic, if you have a reflux baby ask for help. It’s a lot of stress on a parent when a baby cries excessively or cries in association with feeding. What should be a nice bonding time, becomes stress inducing and can really put a negative spin on your motherhood introduction. Friends and family might not know what to do, but will likely be happy to follow your instructions and settle baby for a nap, take them for a walk, or even give them a feed if bottle fed.

If you have a reflux baby or have had one previously, you’ll know how difficult those early months can be. This article is designed to give you information on best practice, so you are fully armed with knowledge when you seek help. It is in no way designed to replace medical advice. Always speak with your baby’s doctor about any concerns, medication changes, or even discuss options around probiotics.


Emma Purdue

Emma is the owner and founder of Baby Sleep Consultant, she is a certified infant and child sleep consultant, Happiest Baby on the block educator, has a Bachelor of Science, and Diploma in Education. Emma is a mother to 3 children, and loves writing when she isn't working with tired clients and cheering on her team helping thousands of mums just like you.



Reflux Clinical Practice Guidelines: Joint Recommendations of the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition. Journal of pediatric gastroenterology and nutrition66(3), 516–554.

Barron J. J., Tan H., Spalding J., Bakst A. W., Singer J. (2007). Proton Pump Inhibitor Utilization Patterns in InfantsJ. Pediatr. Gastroenterol. Nutr. 45, 421–427. 10.1097/MPG.0b013e31812e0149

Belei, O., Olariu, L., Dobrescu, A., Marcovici, T., & Marginean, O. (2018). Is It Useful to Administer Probiotics Together With Proton Pump Inhibitors in Children With Gastroesophageal Reflux?. Journal of neurogastroenterology and motility24(1), 51–57.

Blank M. L., Parkin L. (2017). National Study of Off-Label Proton Pump Inhibitor Use Among New Zealand Infants in the First Year of Life (2005-2012)J. Pediatr. Gastroenterol. Nutr. 65, 179–184.

Dipasquale, V., Cicala, G., Spina, E., & Romano, C. (2022). A Narrative Review on Efficacy and Safety of Proton Pump Inhibitors in Children. Frontiers in pharmacology13, 839972.

Hussain S, Kierkus J, Hu P, Hoffman D, Lekich R, Sloan S, Treem W. Safety and efficacy of delayed release rabeprazole in 1- to 11-month-old infants with symptomatic GERD. J Pediatr Gastroenterol Nutr. 2014 Feb;58(2):226-36.


  • I have a newborn who I thought had reflux and I’ve been begging my doctor for medication for weeks, but he turned 8 weeks this week, and I think we’ve turned a corner. I’m better at settling him, and he is more settled. He has never lost weight, or had any medical issues, he’s just been fussy and difficult, people kept pushing me saying it was reflux. But he’s coming right, I’m so pleased I haven’t gone down the path of medication he possibly doesn’t need. I’m going to try a probiotic this week, thank you for this info.

    Averil Wilson on

  • My son had GERD, and I was so happy when my doctor took the time to rule out other complicatiosn before recommending a trial of omeprazole. I’m a pharmacits and know the risks and complications of a PPI, so was very happy we did things in the right order. Great article.

    Samantha Western on

  • Thank you for this explanation, I was sure the Losec was making my baby worse and my GP wouldn’t listen when I said I wanted to trial no dairy for a few weeks instead. I did it anyway and now my baby is off her medication and happier, much happier.

    Jemma Richardson on

  • Thank you so much! You recommended we try that probiotic a few weeks ago and it has been life changing for our 6 week old. She is now 8 weeks and so much happier. It took patience but we got there and she definitly didn’t have GERD like I thought.

    Robyn Delaney on

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