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Why You Should Think Twice before Giving Your Child Antibiotics


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Antibiotics are necessary and can even save lives, but they are also overprescribed and misused. When antibiotics are prescribed to children for viral (rather than bacterial) illnesses, they are ineffective and can cause lifelong changes to gut bacteria, metabolism, and the immune system. Read on to find out when antibiotics are appropriate, and learn strategies to reduce the need for antibiotics and to protect your children’s microbiome and future health.

antibiotics for kids
Antibiotics for kids are sometimes necessary, but are often over used. istock.com/Kontrec

Antibiotics are among the most frequently prescribed medications for children. One out of every five pediatric acute-care visits resulted in an antibiotic prescription (1). By age 20, the average American child has received 17 courses of antibiotics (2).

Unfortunately, overuse of antibiotics starts even earlier. In the U.S., about 40 percent of women get antibiotics during delivery, just as their babies are acquiring their crucial microbes. To top that off, most American-born babies are given an antibiotic immediately following birth. This was a historical practice designed to protect a newborn from eye infections if the mother had gonorrhea, but it is now regular practice, regardless of the mother’s STD status (3).

The worldwide rise in antibiotic resistance has alarmed the medical community. Pathogenic bacteria are becoming resistant to antibiotics. (4) Potentially dangerous bacteria that are immune to antibiotics could become “super bugs” that have no cure.

Fortunately, some doctors have cut back on their use of antibiotics and now prescribe them only when strictly necessary. However, as a parent, you still need to be watchful when antibiotics are prescribed to your children.

Many Childhood Illnesses Do Not Benefit from Antibiotics: Colds, Ear Infections, and Sore Throats

Antibiotics kill bacteria, not viruses. Nonetheless, many doctors prescribe antibiotics for childhood illnesses that are viral, meaning that antibiotics are unlikely to have any effect.

The two most common reasons for pediatric antibiotic prescriptions are upper respiratory infections and ear infections, of which 60 to 73 percent are estimated to be viral (5). Most childhood sore throats are caused by viruses too. Let’s take a look at each of these separately.

Upper respiratory infections (URIs) such as the common cold or the flu are mainly caused by viruses. As many as 80 percent of URIs are viral in nature and can be traced to microbes such as rhinovirus, parainfluenza, and metaphenumovirus (6). Antibiotics target bacteria only and have no effect on the outcome of viral infections. One study showed that antibiotics were prescribed about 57 percent of the time for acute respiratory tract infections despite the fact that only 27 percent were bacterial. Extrapolation of this data leads to an estimate that there are up to 11.4 million unnecessary prescriptions for antibiotics every year! (5)

Ear “infections” don’t necessarily benefit from antibiotics either. A recent systematic review found that 24 hours after the start of treatment, 60 percent of children had recovered from their ear infections, whether or not they received an antibiotic. Children in the antibiotic group were also more likely to experience adverse events such as rash, vomiting, or diarrhea (7).

When are antibiotics appropriate for children?

When researchers compared immediate antibiotic treatment to a “wait and see” approach, there was no improvement in pain associated with ear infection at follow-up visits and no difference in ear abnormalities or symptom recurrence. This makes you question whether antibiotics help at all in these cases. Antibiotics were most useful in children under age 2 with bilateral ear infections and discharge. In most other cases, a wait-and-see approach was best (7).

In fact, the medical term for “ear infection” is otitis media, which literally means “middle ear inflammation.” It does not necessarily indicate an infection. Some cases may actually be caused by food allergies or food sensitivities, most commonly to dairy products (8). Ironically, treating these cases with antibiotics may alter gut bacteria and further increase food sensitivities.

Sore throats shouldn’t typically be treated with antibiotics, either. In children under 5 years old, 95 percent of sore throats are viral. In older children (ages 5 to 16), 70 percent of sore throats are viral. (9) In fact, only 20 percent of sore throats are thought to be caused by bacterial infection. (10) The bacteria that most commonly leads to sore throat is group A B-hemolytic streptococcus, but up to 30 percent of healthy people carry this bacteria without any problems. Most sore throats will clear up on their own and do not pose serious after effects. (9) Martin Blaser’s book, Missing Microbes, summarizes more of this research. (2)

Why We Shouldn’t Take Antibiotics so Lightly

Overusing and misusing antibiotics has long-term consequences for children’s health. When you take an antibiotic by mouth, it is absorbed in your gut and enters the bloodstream.

Once in circulation, it travels to all of your organs and tissues, destroying bacteria wherever it finds them.  Broad-spectrum antibiotics are especially adept killers, targeting a wide variety of bacteria, including many beneficial microbes. As you can see, oral antibiotics are not a very precise treatment. Regardless of where the infection might be, they affect the entire body and they take out a lot of innocent bystanders.

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Four long-term risks of childhood antibiotics


#1. Changes to the gut microbiota
Every day we are learning new things about the human microbiome, which outnumbers the cells in our bodies ten to one. Seventy percent of the immune system resides in the gut (11) and the microbiota collaborate with the immune system to protect and defend us.

Gut bacteria influence:

  • Immune function
  • Metabolism
  • Nutrition
  • Detoxification
  • Inflammation
  • Weight gain

A recent study (2016) showed that one single treatment with antibiotics leads to serious and long-term changes to the gut microbiota. In Finnish children, a single course of macrolide antibiotics caused major changes in the gut microbiota, and these changes were not reversed until nearly two years after the antibiotic course was completed. (12) Macrolide antibiotics include erythromycin, azithromycin, and clarithromycin.

The study showed that children who took antibiotics had:

  • Lower Actinobacteria, including Bifidobacterium, which is a beneficial gut bacteria commonly used in probiotics. (13)
  • Higher gram-negative phyla Bacteroidetes and Proteobacteria, which are thought to be opportunistic pathogens.
  • Lower bile-salt hydrolase (BSH), an enzyme that mediates host-microbe communication and has been shown to play a role in cholesterol metabolism and weight gain in mice. (14)
    Higher macrolide antibiotic resistance, meaning these antibiotics may not work later in life.

Not only that, but the diversity of the microbial communities didn’t return to normal until approximately two years after the antibiotic course. This means that most children’s gut flora do not have time to recover because two years is longer than the average time between courses of antibiotics (1.5 to 1.8 doses per year). (12)

For more on this topic, see my article on how antibiotics affect our gut flora.

The impact of antibiotics on gut bacteria might be directly or indirectly related to the higher rates of inflammatory bowel disease, asthma, allergies, and impaired metabolism that we see in children who are given higher levels of antibiotics.

#2. Gut inflammation
A study in Denmark showed that children who develop inflammatory bowel disease (IBD) are 84 percent more likely to have received antibiotics in their lifetime.  Children who had taken antibiotics were more than three times as likely to develop Crohn’s disease (CD) than those who had never taken antibiotics, and each individual course of antibiotics was associated with an 18 percent increased risk of CD. (15)

#3. Asthma, eczema, and allergies
Asthma was almost twice as likely to develop in children who had received antibiotics in the first year of life than those who had not. The risk was highest in children receiving more than four courses of antibiotics, and especially those receiving broad-spectrum antibiotics like cephalosporin. (16) Antibiotic use in the first year of life is also associated with rhinoconjunctivitis and eczema in children. (17)

Both antibiotic use during pregnancy and early-life antibiotic use have been associated with increased risk of food allergies. The risk of food allergy increases with the increasing number of antibiotic courses. (18, 19).

#4. Metabolism and weight
Antibiotics also have an impact on metabolic health and body weight. Early life antibiotic use increases a person’s risk of being overweight in later life. (12) Fecal microbiota composition in infancy can predict whether a child will be overweight or normal weight at age seven. (20) In animals, even a short-term disruption to the microbiota from antibiotics changed gene expression in the small intestine and led to lifelong changes in body composition. (21)

Thanks to the gut flora, early life appears to be an especially critical period of development for the metabolism and the immune system, during which time even short-term disruptions can have lasting effects. (22, 23)

Lower Your Child’s Antibiotic Prescriptions with These Five Simple Steps

The most important step you can take toward reducing antibiotic use in your children is preventing the need for them in the first place. Here are five key steps you can take to do that:

  1. Feed them a nutrient-dense, whole foods diet to reduce the likelihood, frequency, and severity of childhood infections.
  2. Have your children wash their hands frequently to reduce their exposure to infectious germs. A good habit to get into is washing hands just after they get home from school or other outings, in addition to the typical times (before meals, after using the bathroom, etc.).
  3. Give them supplemental nutrients that can prevent or shorten the duration of infections
  4. Encourage their consumption of fermented foods and fermentable fiber to support gut health, and consider supplemental probiotics and prebiotics.
  5. Consider botanical remedies that can shorten the duration of viral infections, improve immunity, and provide symptom relief.

If your doctor does prescribe antibiotics, ask if he or she is certain that the condition is bacterial in origin and whether the condition requires antibiotics or may safely resolve on its own without them. “Watching and waiting” is a valid strategy that is often preferable to treating with antibiotics prophylactically.

That said, there are times when antibiotics are necessary. If you and your doctor determine there is a good reason for your child to take them, there are things you can do to reduce the long-term effects. These include taking probiotics and prebiotics, consuming bone broth, and supporting healthy liver detoxification.

I hope this article has made it clear that antibiotics should be given only after careful consideration, especially if the condition your child has is likely to be viral. Antibiotics have a time and a place, but since they can have wide-ranging effects on the gut flora, metabolism, allergy, and inflammation, they should be used with discretion.

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Join the conversation

  1. You closed the article with advising proper liver detoxification in the event antibiotics are used. What exactly does that look like for and infant, child? Is it safe to give them milk thistle? Are there safe herbal teas that kids can take and help cleanse the liver?

  2. I’ve had chronic bladder infections as a child and were put on course after course of antibiotics. I truly believe this set me up for a lifetime of chronic health conditions such chronic strep throat, yeast over growth that started a 6 year battle with vulvadynia and now dealing with chronic idiopathic urticaria from the countless food allergies I have developed over the years. I truly believe I was set up for all of this by the countless courses of antibiotics that were dished out to me 45+ years ago.

  3. I was given Levaquin in the ER for a kidney stone, I assume they thought I had an infection. Five IV bags later I have a torn rotator cuff a torn meniscus, peripheral neuropathy , spinal stenosis , ringing in the ears, brain fog and high anxiety. I was never given any information on the adverse reactions that could come from being given this medication. These are life changing reactions to a medication that does not have the proper warnings for doctors. Thousands have died from these drugs, thousands are suffering , thousands need help, thousands deserve to have their lives back. I want my life back….. don’t ever take these drugs, there’s too may other antibiotics doctors can prescribe.

  4. My life was ruined by this drug. I can no longer work because of what this did to me. I took it multiple times and each time I got worse and worse. It started out with a delayed reaction, tendons in my feet and ankles were all messed up so I had to wear wraps to work. I also started getting pretty severe and very frequent headaches and migraines, along with back pain and weakening muscles. The pain got so bad I had to start taking pain killers after a while which I was on for so long that I was getting addicted and they didn’t even really help after the pain got so bad, so I got off of them. Now I live and suffer with the pain, and nothing even takes the edge off anymore. After the other doses I started noticing increased anxiety and decreased energy lvls. My headaches got more frequent and more painful, and I started getting pain in my eyes, leading me to believe I had MS after yrs of not being able to find any other explanation (this was before I found out that fluoroquinolones could cause this). I also started getting nerve pains, pinched nerves from my crumbling bones and crippling arthritis that was progressing a lot faster than any other person’s arthritis I’ve ever seen. My bones in my back and hips are a mess (they look like swiss cheese) and are starting to fuse together. I have liver, kidney and heart problems, the list goes ON AND ON! I can never be comfortable again, and now I can’t even do what I love to do, which is spend quality time with my kids and cook for my family and host parties. I had a passion for cooking and helping ppl, and I can’t do either of those things much anymore. I was going to college and had to drop out because of anxiety, and increased cognitive decline keeping me from doing the timed tests I had to take. As I said, my life is ruined now, and it all started with fluoroquinolones. I can never get justice either because I took a generic brand and I can’t sue because of that….. Thanks America, you have failed me once again! F*** the FDA!!! It’s corrupt and indecent in it’s practices, making it too easy for crap products to be pushed through! They, along with the pharmaceutical companies, have been poisoning us for decades! (Pharmakon- A Greek word, the origin for the word pharmaceuticals, meaning poisonous cure.)

    • Kyah , i just read your story. I’m sincerely sorry that bad meds did this . I had a simple experience about 25 years ago. I hope that you get better and better.

  5. Sadly, Fluoroquinolones are given to kids and babies all the time in the form of ear and eye drops. Ciprodex is even worse as it’s a steroid and an FQ. I was floxed by that combination and it nearly killed me. Not to mention the near 100 side effects I received. You would never trade out a minor infection for the inability to walk, neuropathy, kidney damage, thyroid damage and on and on.

  6. Thank you! This is a fantastic article! I was horribly damaged by the synthetic antibiotic Levaquin, which has been in the news quite a bit lately. The fluoroquinoloes (FQs) are the most prescribed class of “antibiotics” but they are actually chemo agents, so the damage they do is systemic, from head to toe, body and mind. It is impossible to exaggerate just how horrific it is to have a chemical melting your collagen and dissolving your DNA. I urge everyone who reads this to google Levaquin or Cipro and either news or damage or problems; you will be stunned at what you find. I admin in Fluoroquinolone Toxicity Group;; join us if you think you or someone you take care of have been harmed. Best wishes!

  7. I am a 30 year old woman who was also on prescribed cold related antibiotics 2-3 times per year throughout most of my adolescence and early adulthood and I was also born by c- section. I’ve struggled with acne and a sluggish metabolism. I haven’t used antibiotics in over 4 years, but now I’m wondering what advice and resources there are to start preparing my body for pregnancy. Is there testing to see what bacteria, microbes, and minerals I’m missing?

  8. Dr. Kresser, thank you so much for posting such an in-depth and much needed piece on antibiotics overconsumption and children. I am in my final weeks of graduate school, studying to be an integrative nutritionist specializing in women’s health and early childhood and this article could not have come at a bette time!

    I am blown away by the amount of information that the public is lacking on the overuse of antibiotics in small children. Reading your article I was literally shaking. My son, who is now 3 years old was breastfed for 2.5 yrs, was rarely sick and healthy baby for the most part. Once I weaned, he started to eat more allergen foods and took his first dose of the z-pack three months later for a cough his pediatrician scared me into thinking could or was developing into pneumonia. Two or three months later, he was diagnosed with otitis media with effusion and was treated again with antibiotics, this time amoxycillin to which he had a delayed reaction that resulted in a nasty rash reminiscent of 5th disease all over his body for over 6 days.

    It is now March, nearly six months since his OME diagnosis and my little guy is still presenting with the effusion, which any cold or virus seems to only ascorbate, though luckily we have found a integrative ENT and homeopath who are helping us heal his body in order to avoid myringotomy.

    I plan to print multiple copies of this article to share with family and his pediatrician so they know I am not crazy in the amount of research I have done on my own to find the root cause of his OME aside from underdeveloped eusthecian tube anatomy.
    Thank you from the bottom of my heart for this important and powerful piece. Knowledge is power and the bette we are informed, the better we can serve and take care of our children and their future as it pertains to their health.

  9. Yes, my son was fine until I returned to work st 6mos old part time, and went from breadt milk to some milk based formula. He showed signs of milk allergy in hindsight but Doctor did not make connection. Pink rashly cheeks, ear infections, colds, and one round of antibiotics after another. She also told me to give him Dimetap to relieve congestion, even though he was well under recommended age. Later this drug was pulled from market and reformulated. With all of this stuff in his body I would say he must have had mytochondrial dysfunction. Add vaccines / toxicity on top of all of this given to a very sick baby. CDC head is in camera talking about increased risk of autism linked to vaccines in children with mitochondrial dysfunction. He is Autistc with global delay / MR. 17 now. Will need life long care. I don’t blame the doctor, but really the medical industry is just so messed up these days… Little health resulting from pediatric medicine that is so focused on despencing pharmaceuticals. We need to be super informed and advocate for our children to stop the poisoning of our children.

    • Forgot to mention at 14 mos he was given MMR (this baby was already sick) and then hospitalized within three weeks with severe intestinal distress/dehydration. Had terrible stuff /poop coming out of him after that for months/years. Fevers spiked to 105 often, and out of no where. His gut and immune system messed up after that. It was not until I said no to all vaccines, antibiotics, drugs, artificial anything, and did protocol to heal leaky gut that he got well. But the damage was done and so far he continues to have neurological issues/autism.

  10. I know of 4to6 young adults, thirty-ish. Some with repeated antibiotics as young children. They have struggled with addiction, eating disorders, various levels of mental illness. It would be very interesting to track mental illness tendencies ,in those who started out very young, with disrupted gut Bacteria. Also, throw vaccinations onto the mix, for even more threads to follow.

  11. My 10-year-old son had a severe infection on his finger around his nail and was given antibiotics (7 days of 500 mg of amoxicillin twice per day). Although I rarely allow my children to be prescribed antibiotics, I was very concerned about the condition of his finger causing further problems. We had tried topical treatments but nothing was working. What could we have used instead of antibiotics in this case?

    • I have used essential oils in cases like this. Oregano is excellent along with lavender. You can put those in some coconut oil and place a bandage around it is needed 🙂

    • Good old fashioned sea salt and the hottest water you can stand. Repeated soakings and dipping the finger. Works like magic!

    • My daughter has this happen from time to time and our pediatrician recommends soaking her hands in warm Epson salt water each day to draw the bacteria out. Has worked so far, reduce the redness and inflammation.

  12. Hi.
    There are NO pathogenic viruses and NOBODY has any evidence in the form of proof otherwise. There is a big court case in Germany right now about the proof or lack thereof concerning “measles viri”.
    However, if the present medical establishment believes in pathogenic viruses and does NOT administer antibiotics as a result, then this is a good thing! Ignorance is bliss.

  13. wonderful article that i have shared with my clients. thank you. just wanted to suggest an addition to your suggested alternative approaches – homeopathy, an alternative form of medicine that has been in existence for over 200 years that has a clinically proven track record in the treatment of many diseases, including URTIs. what a wonderful world this would be if we truly embraced the concept of integrative medicine and recognised that all forms of medicine and approaches to health have a vital role to play. and yes, in the spirit of disclosure, i am a homeopathic practitioner with a firm belief in the statement that without fertile soil, there can be no germ theory – nutrition and homeopathy both have a vital role to play in strengthening the soil ie our body.

  14. I was prescribed antibiotics for acne in my early teens for 18 months (argh!) Over the past 20 years I’ve had chronic thrush, digestive issues, fibromyalgia and by far the worst – vulvadynia… from reading articles on websites such as this (thank you Chris!) and speaking to integrative practitioners it seems very possible that the effect antibiotics had on my gut was profound and led to this myriad of issues. I agree that they should only be used if absolutely necessary and at the same time doing everything you can to support the gut.

  15. I have Crohn’s disease and believe that all the antibiotics I took as a child is the reason. I was a chronic ear infection kid who took antibiotics every time. I was taking them at least 6 times a year from the age of 1 till my late teens. My Mom was a smoker too which didn’t help because it probably contributed to the ear infections.
    I do things much differently with my 4 children, all were breastfed giving there digestive system the best possible start. We eat healthy locally grown fruit, veggies, and meats and take probiotics. We have also added bone broths to our souls and stews. All but 1 of my children have only needed antibiotics 1 time which was for strep throat. My oldest is 15 so she has had antibiotics more than once for strep and an ear infection. I always take the wait and see approach since I am an RN and personally see he devestating effects of antibiotic resistance.
    Living with Crohn’s has not been easy and if only my parents had known then what I know now it could have been different for me.

    • There is evidence linking use of antibiotics, and other medications like Accutane, and IBD. Unfortunately, parents and their kids are rarely advised of these risks.

    • Great article. Thanks

      I just wanted to say that I developed countless and countless of debilitating damages, diseases and diagnosis’ that star.ted m 3 years ago right after taking Cipro XL for 9 days … 1 pill a day (in the Fluoroquinolone Family of Antibiotics) for a suspected UTI infection, which I did not even have. I had 90% of the listed adverse reactions that still continue to add up today.

      These Fluoroquinolones (FQs) are the most common antibiotics and sadly are given to people of all ages and in perfect health who initially only had a minor bacterial infection and ended up severely debilitated and worse in excruciating chronic non-stop pain 24/7. I just recently learned that now they even give it to women who after they birth delivery through IV just in case they develop a UTI, which the nurses tell the mother’s. Ive actually even met a young 25 year old mother with a few month old baby, who was given Cipro and she had no idea why and how she is so sick with multiple damages until I asked her if she took Cipro – was a shock to her and I am sure she’s done her research as this was early winter. In my area where I live, I have crossed paths with 100s and 100s of FQ victims who had no idea that they or their family member possibly became severely ill from these FQs. Most FQ victims do not relate their damages to FQs because in many cases their first adverse reactions start coming out after about 7 months of stopping the FQ or if they react right away the adverse reactions are so bizarre that you would never think that 1 pill or even 30 pills can do such severe and unusual immediate damage. Google “Cipro Toxicity” or “Fluroquinolone Toxicity”, etc. in youtube and google to educate yourself to Know to say No to all Fluoroquinolones. There are other drugs that are damaging too, but taking FQs is like having an atomic bomb going off in your body.

  16. What if it is confirmed strep throat in a child (with symptoms)? Do you recommend antibiotics then? Thanks!

    • please allow me to answer that question with one perspective. i am a homeopathic practitioner that has successfully treated the symptoms of strep without the need for antibiotics, on more than one occasion. however, whichever approach you choose, the most important thing is that you feel comfortable with that choice. for some of my patients, the antibiotic path is still their first port of call and in those cases, the combination of nutrition in conjunction with homeopathy can assist bring the body back into balance, with the negative impact of the antibiotics being akin to introducing another layer of disease. in other words, whilst antibiotics may lay to rest the bacterial infection, they simultaneously strip the body of beneficial bacteria and therefore weaken the whole organism (i refer you back to this eloquent article). in relation to my own family’s health, i would always try the botanical, nutritional, homeopathic approaches first and would only consider a pharmaceutical option if these approaches failed – to date my children have never required antibiotic treatment and they are now 23 and 17. however, i also believe that antibiotics have an important role to play and their value should never be underestimated.

  17. This is a great article. Unfortunately, prescribed antibiotics are not the only ones affecting our micro biomes. They are given to animals and end up in the meat we eat, the milk we drink, the water we drink. Many GMOs, pesticides and herbicides, such as Roundup, are antibacterial in nature and also wrecking havoc. Another way to safeguard your family is to be eating an organic, preferably local, whole foods diet.

    • Absolutely. I think antibiotic residue is the primary reason (among several others) to eat pasture-raised, organic animal products.

  18. Thank you for this article. I made the mistake of allowing antibiotics when my child was one year old. Granted my child was super sick and I had to rush her to emergency but the doctor did zero tests. I asked “are you sure it’s bacterial?”. No hesitation “yes”. He was a top doctor in my region and not used to being questioned. I couldn’t even get the antibiotic to stay down because it kept causing her to vomit but enough got in to start a big problem. (The antibiotic did not improve her condition at all so I know it was a viral issue.)

    So right after that the ear infections started, and were a constant problem which of course the doctors prescribed ever more antibiotics (when it was so bad that I felt I had to see them). Yeah I’m a” thinking” mom but one also panics when a kid is so sick. So then I was told “she’s aboriginal so predisposed to ear infections. She’ll probably need tubes”. I knew that was bunk.

    Fortunately when my child was four a friend of mine told me about tamanu nut oil, and we had recently started eating a better diet as well. The tamanu nut oil is AMAZING. At the first sign of any soreness I put a couple drops in the ear and in four years my child has not had one single ear infection. It’s gone before it even develops and the oil does not sting (unless it gets in your eye-I don’t recommend that!). So diet first and foremost, but don’t dismiss medicines found in nature as well.

    Additional note: breastmilk is also very anti-bacterial. I refused the eye drops when my baby was born and when one eye became infected I searched online about natural treatments. Aboriginal people all over the world know to use breastmilk; what happened to our knowledge? Wiped out in just a couple generations of Big Food and Big Pharma.

  19. I am so glad you wrote this article but what are your feelings on topical ear and eye drops? They are just as dangerous yet doctors feel they do not go through one’s system like the pill or IV form. I have been very harmed by the Fluoroquinolone ear soluton at age 62 and getting worse as the past 3 years have gone by. I already had a hypersensitivity with FQs. I am afraid kids are getting too much of the drops and it is harming them as well.

  20. Excellent and comprehensive as always. Our 9 month old was in hospital with bronchiolitis for about a week when she was first born, at which time she was given a course of antibiotics. This was also being born via a c-section (both of which impact on the microbiome). Since then she started having severe outbreaks of eczema. We have since given her lots of bone broth, some fermentable foods and removed dairy and gluten and her eczema has improved dramatically.