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Medical Reasons Baby Won’t Sleep: 5 Things To Look For

It’s the middle of the afternoon. I’m vigorously rocking 6-month old Baby Z back and forth, trying to convince those beautiful baby blues to drift shut.

Little Man E, my 2-year-old, is sleeping soundly down the hall — like he always does.

I had planned to use this time to: do laundry, shower, load the dishwasher, finish hanging the baby pictures, text a friend, or maybe just put my feet up for a few minutes. Oh, who am I kidding? I’m not sure why I ever count on Baby Z napping so I can get some “me” time.

Baby Z has been a horrible sleeper from day one. Here I was, on child #3, and I was at a complete loss. I’ve read ALL. THE. BOOKS! I’ve consulted the Interwebs. I’ve stalked Facebook groups. Nothing I tried on this kid (and certainly nothing that worked with my other two) would actually get him to successfully drop those long, feathery lashes and sleep.

None of my three beautiful children started out as great sleepers. I’ve worked really hard at creating healthy sleep habits and schedules for them. But sometimes our baby’s might have underlying medical issues that are preventing them from settling into a good sleep pattern.  Here are 5 medical reasons your baby won’t sleep.

Keep in mind, that I’m not a doctor and am not giving you medical advice below.  Really, all I’m trying to help with are ideas if you’re as perplexed as I was.  Always consult with your doctor to discuss any of your baby’s medical concerns.  

Reason 1: Allergies and Intolerances 

Food allergies and sensitivities are on the rise. According to, 1 in every 13 kids has some form of food allergy….and this doesn’t even take into account those that experience symptoms but has yet to be diagnosed.

My middle child was the picture of a perfect birth. He showed up around 38 weeks (just as I was starting to think, “Okay, buddy, you can come out now.”). I had a quick easy labor and effortless delivery (well, as much as birthing a child can be effortless).

But about 4 weeks in, my perfect man started showing signs of colic. He had frequent hiccups, lots of uncharacteristic drooling, excess spit up, and a diaper rash that just would NOT go away. And, of course, no sleep. Through research and previous experience, I started an elimination diet. Because I was nursing, I removed things from my diet that are known as common allergens — like dairy, soy, wheat, corn, etc. This process helped tremendously.

There are two formal names for food/milk allergies

But his symptoms persisted and we learned he had a condition known as FPIES (Food Protein-Induced Enterocolitis Syndrome). A similar condition is called MSPI (Milk/Soy Protein Intolerance). This type of food allergy is often overlooked because it is not an immediate reaction. The good news about FPIES or MSPI is that it CAN be managed and most children will outgrow the symptoms by the age of 3 to 5.

How an allergy affects sleep

Any food allergy or intolerance will absolutely affect your child’s sleep because it causes extreme discomfort in the digestive tract (think heartburn, vomiting, stomach ache, diaper rash, etc.). If you suspect your child has a food sensitivity or allergy, you should consult your pediatrician. But since not all pediatricians are equipped to diagnose such a new phenomenon, don’t be shy about attempting an elimination diet. There are great resources online to help.


I’ve read ALL. THE. BOOKS! I’ve consulted the Interwebs. I’ve stalked Facebook groups. Nothing I tried on this kid (and certainly nothing that worked with my other two) would actually get him to successfully drop those long, feathery lashes and sleep.


Reason 2: Reflux 

Infant reflux, according to my research, is fairly common. Which makes sense. When babies are born, their lower esophageal sphincter is still immature and will allow contents from the baby’s stomach to flow back up into the esophagus. It’s not a problem unless your baby is experiencing troublesome symptoms — like poor sleep.

Signs of reflux include arching, squirming, and screaming.

I first suspected reflux when my firstborn was around 4 weeks. It seems so long ago, but I clearly remember the exhaustion. All the experts vehemently recommended swaddling your baby and putting them on their back to sleep. But my precious peanut was having none of it. She squirmed and grunted and writhed continuously all night long. As a new mom, of course, I would bolt awake at each little sound.

Baby Peanut would spit up forcefully with each feeding (so much for my brand new suede nursery rocking chair) and scream inconsolably for about 45 minutes after each feed. And put her down?? Not a chance!!

As always, if you suspect your babe has reflux, you should contact your pediatrician. Our doc does not believe in medicating infants for reflux unless they aren’t growing normally or are showing other signs of distress. And looking back, I’m glad for his advice.

Do you have an over-supply issue?

We managed my daughter’s condition by reducing the amount of milk she was getting at each feeding. As a first time mom, I was freaked out about my supply and worried I wouldn’t be able to tell if she was getting enough to eat. Come to find out, I had (and always have had) a serious over-supply issue. It led Baby Peanut to over-eat and become extremely uncomfortable. So I tried block feeding (feeding on one side for several feeds) until my supply was normalized around 5 months.

Keep the baby upright after feeding.

Another tip that we did was to keep sweet babe upright for about 30-45 minutes after eating. This meant a lot of babywearing (which I honestly did not mind in the least — extra baby snuggles) and a couple of extended late-night rocking sessions. I got really good at sleeping sitting up in that wrecked suede recliner!

Many people have luck keeping the crib or bed tilted so the baby’s head is above her feet. This is great advice if you can get it to work. Sadly, we had a hard time with Baby Peanut sliding down into a heap at the bottom of the crib.

Reason 3: Chiropractic adjustment  

Many times babies are born fussy or have trouble feeding, sleeping, or with their digestion. If there is nothing medical causing the issues, parents will turn to a chiropractor for help. I have had great success adding my good friend and pediatric chiropractor to our team of baby care experts.

Now, chiropractic care is not for everybody. But if you can find a chiropractor who is well-trained and knowledgeable about infants, perhaps a minor adjustment can help a fussy baby feel better.

The theory behind chiropractic care for the newborn is that it’s easy for things (“things” is, of course, professional, medical-approved terminology) to get shifted in their journey out the birth canal. Consider when you sleep with your neck or back at an odd angle and the pain and reduced range of motion you might feel the next morning.

A skilled chiropractor might be just the ticket to relieving some of your baby’s discomfort. Always discuss with your child’s pediatrician before taking your babe in for any “work.”

Reason 4: Adenoids/Sleep Apnea 

Sleep apnea occurs when someone stops breathing in their sleep. A child with enlarged tonsils, adenoids, or other condition that prevents them from getting adequate oxygen during the sleep cycle is not only at risk for sleep issues, but could also be in serious danger of other health issues. If your child snores, breathes heavily when sleeping, or is restless during the sleep cycle, you may want to discuss with your pediatrician whether this might be something that can improve their sleep.

None of my children suffered from this condition, but it came up frequently in my research.

Reason 5:  Autism/ADHD 

Most kids are not diagnosed with Autism Spectrum Disorder (ASD) or ADHD until they are older — usually around age 6 or sometimes a little before. However, these conditions are largely genetic. And studies have shown that infants and newborns with these conditions can show signs very early on.

Many children who are later diagnosed with ASD or ADHD showed these traits as an infant:

  • Squirmy
  • Not very cuddly
  • Impatient
  • Easily frustrated
  • Colicky
  • Difficult temperament
  • Sleep issues

If your child shows these traits, does that mean they will have ADHD or Autism? Absolutely not.

My 6-year-old has ADHD and Autistic tendencies. She is also on the gifted spectrum. She was only slightly colicky and continues to have sleep issues. My third child, however, displays all of these symptoms. (Wonderful, right?)

Children cannot be diagnosed as infants with ASD or ADHD. The point of having this on your radar is for reasons of early intervention. If you can begin to understand and relate to their temperament, you can begin to work WITH them instead of AGAINST them when it comes to helping you both gets some needed sleep.

OK, So Your Baby Has A Medical Condition. What can you do to get your family better sleep?

Now that you’ve pinpointed the reason that none of the regular sleep hacks are giving you OR your babe better sleep, what can you do about it?

Talk to your pediatrician. If your baby has any underlying health issues, you’re going to want someone with some knowledge and tools on your side. If you’re not getting any support from your child’s regular doctor, consider shopping around. Not all pediatricians are knowledgeable in all areas — especially for some of these newer conditions or ones that are harder to diagnose.

(Friendly reminder: this site doesn’t offer medical advice – nor is offering a diagnosis of your baby.  You should ALWAYS talk to your baby’s pediatrician with any medical concerns.)

Keep a journal. By documenting things you ate, things baby ate, tricks you tried, how baby fell asleep, how baby slept, and baby’s activity before napping, you might start to notice some recurring patterns. Pay attention to some of these patterns to see if there are changes you can make to your routine that might aid in better sleep.

Find a support network. Whether it’s friends and family, an online or Facebook group, your church, or a local mom’s group, there are other people out there going through similar struggles. There are people out there with a gentle ear willing to listen as you unload your stress and frustration. There are people out there willing to share stories and tips of things that worked for them. Sometimes knowing you aren’t alone is half the battle.

Practice self-care. This might possibly be the hardest point I make in this article. Making time for ourselves as busy moms is hard — especially when we are juggling a high needs child on little sleep. Even if it’s just 5 or 10 minutes to sit quietly in the bathroom with the door locked while you close your eyes and breathe deep, make sure that you are putting your own oxygen mask on first. If you are stressed and stretched beyond your limit, you’re definitely not going to be doing your baby or your family any good!

Comment Below:  Did your baby have any of the medical conditions above?  What is the best advice if your baby won’t sleep because of underlying health issues?  


Casey Gromer is founder and educator at Simpler Skincare — a business that empowers women to learn and understand the potentially harmful ingredients that may be lurking in their skin and personal care items. When mounting health issues started taking over her family, she began studying the impacts of diet, nutrition, and lifestyle habits on our overall health and well-being.

When she’s not wrestling her 3 bright, beautiful children to sleep, she’s studying integrative skincare, hanging out at the gym, or playing outside.

Need More Help With Sleep?  Keep reading my most popular blog posts:

Baby Only Naps For 30 Minutes?  Short Naps Suck!  

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8 Month Sleep Regression


Susie Parker is founder of Sleep Baby Love and a Certified Infant and Child Sleep Consultant through the Family Sleep Institute. When Susie's not ridding the world of sleepless families, she loves spending time with her two girls that have given her a ton of real world sleep experience head on.

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