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Common Sleep Disruptors: Illness, GI Issues, Medication, Teething

Be sure to talk to your child’s doctor about any medical, physical or teething concerns; this blog is not intended to be medical advice.

Illness, medication and teething can make it very hard for you to know what your expectations should (or shouldn’t) be of your child. And, because sleep is so important to immune function and healing, it’s important your baby stay rested, especially during times of illness. We work with many parents who think their baby has a really terrible sleep problem, when in fact the child has an underlying medical issue that NO AMOUNT of sleep training will solve! Parents and pediatricians can help identify when to expect independent, consolidated sleep, and when to put that independence on the back-burner while managing something medical.

Before starting any sleep training, make sure your child’s sleep problems are about a sleep association and NOT about something medical. How? Assess the pattern of her wake ups AND her physical symptoms with the help of your child’s doctor. Sleep association wake ups tend to be at fairly predictable times-often at bedtime and then, after a long stretch of sleep, every 60-90 mins overnight. Wakeups due to pain or illness tend to be much more erratic and random (ex: every 10 minutes, or at times that are not usual for your baby).

Some children have one severe illness after another and others have months of GI issues to work through. Although frustrating, if your child is frequently sick, or struggles with severe reflux, chronic ear infections or eczema flare ups, you may have a harder time when it comes to sleep than some new parents. You may find it helpful to know when to just accept the stage your child is in and keep her rested in whatever (safe) way you can, and when to raise your expectations when it comes to improving and consolidating sleep. Here are some common sleep disruptors and some basic tips on how to handle them:


The Science: Reflux is common, and often quite controllable with diet and medication. Reflux can also be very painful and uncomfortable for some small babies. Most babies experiencing reflux are too young to begin any formal sleep training.

The Sleep: Babies who have reflux can be great sleepers with time but, only when their symptoms are under control. Reflux is very challenging for parents who find themselves second guessing if their child is in pain. Use your parent intuition, listen to your baby’s cry, and when in doubt – comfort your baby with extra soothing! When pain is under control and if your baby is old enough, you may resume or begin a sleep training strategy to work on any habits that may have popped up during the days and weeks your baby’s reflux was still acting up. Good sleep patterns, age appropriate schedules, and environments should still be practiced even for babies with reflux.

Baby Sleep Science Sleep Tips: Work with a GI specialist who can closely follow your baby’s growth and weight gain and titrate doses of medication as your baby grows (quickly!).


The Science: If symptoms are acute, requiring active intervention by you to keep your baby comfortable (think: sitting in a steamy bathroom, holding your baby upright to ease congestion, frequent and persistent coughing, frequent nasal aspirating and nasal saline to clear small passages, etc) your baby is probably too sick to have high sleep expectations. If your baby has mild sniffles, clear runny nose, or mild occasional coughing with no apparent distress or pain, typical sleep patterns may still be expected.

The Sleep: For acute illness, pause your sleep intervention, treat or medicate your baby as directed by her doctor, keep her rested, and resume your plan when she’s feeling better. If possible, try to hold steady in any progress you already made with your sleep plan. If your baby’s symptoms are mild, continue with your plan as usual. If at any point symptoms change (even in the middle of the night) and become more acute, stop your plan and resume when she’s better.

Baby Sleep Science Sleep Tips: keep your baby hydrated, use nasal saline to keep nasal passages moist, and a cool mist humidifier.


The Science: Pain of any type (whether due to uncontrolled reflux, acute teething, illness, surgery, or injury) and fevers associated with discomfort (usually above 100 F) should be considered sleep disruptors.

The Sleep: Although the timing might not be ideal, if your baby has pain or fever, plan to pause in any sleep intervention you had begun, and give your baby the soothing, comfort, and treatments she needs to feel comfortable. Sleep is good for immune function and healing so keep your baby rested through pain or fever even if it means doing more than your usual amount of soothing. When the pain or fever has resolved, you may resume your sleep intervention. You may be able to pick up where you left off or, if the illness went on for several days and you picked up new sleep associations, you may have to start from scratch.

Ear infection:

The Science: Pain is a true sleep disruptor, which means during times of pain, your expectations for good sleep are lowered significantly. Ear infections are notoriously painful, often more-so when lying down.

The Sleep: With an ear infection diagnosis, stop your plan and/or lower sleep expectations and provide soothing until your pediatrician confirms the infection has cleared (make a re-check appointment after treatment). Sleep training a baby with chronic ear infections can be very challenging because ear infections can pop up with little notice and parents often second guess if baby is comfortable. If your baby is prone to frequent ear infections, try to begin sleep training when your child does not have any cold/congestion which are common precursors.

Baby Sleep Science Sleep Tips: keep your baby hydrated and keep secretions moist by using a cool mist humidifier and nasal saline.

Eczema/Other Itching:

The Science: Itching is disruptive to sleep!

The Sleep: If your child has itchy eczema or other itching rashes or insect bites you’ll want to delay or pause in your sleep training until the itching is under control. A baby with eczema can still be a great sleeper – when the itching is controlled.

Baby Sleep Science Sleep Tips: soothing creams, lotions, and soaks can be helpful for itching as well as natural over the counter remedies. For severe cases, prescription creams provided by your doctor can be very effective, very quickly.

Antibiotics/Diarrhea/Diaper Rash:

The Science: Antibiotics are notorious for causing GI upset. Typically, with circadian rhythm maturation around the 3-4 month mark, overnight BMs stop. With antibiotic use, diarrhea and nighttime BMs may occur. Diaper rash is also common.

The Sleep: Diarrhea or nighttime BMs need to be changed, but a diaper change is very stimulating! When changing a diaper in the night, keep it as dark, quiet and calm as you possibly can and still effectively change your baby. Pile on the diaper cream and pause in your sleep training until nighttime BMs and/or painful itchy diaper rashes have resolved.

Baby Sleep Science Sleep Tips: check with your pediatrician about using a high quality probiotic for your baby if he’s on an antibiotic.

Asthma medications:

The Science: Certain inhaled medications cause feelings of hyperactivity, racing heart, or jitters.

The Sleep: The above side effects can make it difficult for a baby or preschooler to calm and relax himself enough to fall asleep. Use of inhaled asthma medications may affect your baby’s ability to fall asleep on his own at the time you’d like and might require you to pause in your sleep training plan until the underlying symptoms have resolved and medications are discontinued or decreased.

Baby Sleep Science Tips: For children who require long term or frequent use, ask your child’s doctor if it’s appropriate for medications to be administered an hour or more before bedtime rather than in the 10-15 mins before tuck in!

Food Allergies:

The Science: Streaks of blood, and gobs of mucus in the stool may be signs of GI irritation. These could be due to any number of common issues (like rapid letdown, foremilk/hindmilk imbalance) or, most frequently due to a milk protein allergy. Other common allergies are egg, wheat, soy, and nuts. Breast feeding mothers may go on strict elimination diets to be able to continue nursing their baby with an allergy. In some cases, hypoallergenic formulas are used.

The Sleep: Occult blood and mucus alone do not necessarily mean your baby is in pain, but if your baby IS in pain, well, you know the drill. Pause in any sleep training, provide extra soothing and comfort to facilitate adequate sleep and work on improving things when you baby is feeling better.

Baby Sleep Science Sleep Tips: Work closely with a GI specialist who can help you manage your baby’s allergies and who will support you in continuing breastfeeding your baby if you’d like to do so. If you have been trying solid foods with your baby and s/he has a history of GI issues, please don’t introduce any new foods during the time you are working on a sleep training plan. Stick to familiar favorites and foods you know are not irritating to your baby.

o If you live in the Boston area, Meg recommends Dr. Garrett Zella for pediatric GI issues.


The Science: Your child will teethe on and off for two years and then some! For the most part, teething is not as big an issue as parents think when it comes to sleep. Any potential pain associated with teething is usually as the tooth is coming up through those sensitive little nerve endings at the gumline. If there is pain with teething, it’s generally not for more than 3 days, certainly not weeks on end.

The Sleep: That said, some babies are harder teethers than others and some teeth are harder to teethe than others (incisors and molars usually). Teething may disrupt sleep for 1-3 nights, but if you find yourself blaming night wakings on teething for more than a few nights in a row it’s either (1) probably not about teething or (2) it was about teething and now has turned into something else, such as a new sleep association.

Baby Sleep Science Sleep Tips: If you can’t see a tooth anywhere in sight, teething is probably not the culprit. Mouthing, drooling, chewing on toys or hands are developmentally normal pastimes for babies ages 5 months + and shouldn’t necessarily be interpreted as teething. Assess your baby’s mouth before bed. If his gums seems swollen, red, and painful and you see a little tooth about to erupt – pain may very well be the cause of an unsettled night. If your baby has no signs of active teething and is simply drooling or chewing on toys more than usual teething is an unlikely culprit for disruption.

Sleep Disorders

True sleep disorders are rare in infants and toddlers. The most common “red flag” we see in young children is snoring that is unrelated to congestion or positioning. If your child chronically snores, his airway should be evaluated and risk of sleep apnea assessed by his pediatrician (and probably a specialist as well before beginning any sleep training).

How we can help:

Even if your child has reflux, allergies or other more serious medical conditions, we can still help! There are many building blocks to good sleep that can be implemented such as sleep timing, sleep environment, routines, and using sleep associations to help establish patterns. With many conditions, some very interactive sleep training approaches can help improve sleep while waiting for medical clearance to begin something more structured. Ask us a question on Facebook or schedule a consult-find out how we can help!

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