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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. As a teen I was prescribed long term antibiotics for acne, these courses went on for months at a time over a period of about 3 -4 years. I’m now 47 and I find myself in all sorts of digestive trouble ( low acid, poor digestion, poor assimilation of nutrients, IBD, slow motility, fatigue depression etc etc. this affects my moods and the quality of life in general. I’ve tried all sorts of things but I don’t think I’ll ever be right.

    • Terry, don’t give up hope! All your comments sound very familiar to my problems. I am much improved, through trial and error, I now eat a limited range of foods.
      Eliminated are all nightshades, grain fed red meat (can eat white meats) ALL grasses including sugar, wheat, rice etc, lettuce, sunflower and sesame (which is in many processed foods) and processed meats.
      Look at alternatives and good luck.

  2. I was given years of antibiotics for acne. Then I got an MMR booster in college (while still on antibiotics) and my health went downhill from there. I attribute all of my chronic issues to those 2 things. I have been trying to figure it all out and repair it ever since.

    Then recently I took my sick 4 year old to urgent care where a very uncaring doctor told me he had an ear infection and that the ONLY thing we could do for it was 10 days of antibiotics! I was appalled and knew better. He was fine the next day (no antibiotics of course). It made me so angry that he could be so careless with a child.

  3. You are completely right ; I am fortunate enough to be aromatherapist so essential oils are my usual powerful tools to avoid completely any visit to a doctor. We haven’t used any antibiotics for years! Some of my clients are doctors, and dentists, who learn from me how to replace antibiotics with essential oils. It simply works.

  4. Chiropractic adjustments regularly for both my kids and essential oils daily has kept them relatively healthy.

  5. I have an issue with the way this information has been presented. Perhaps a less “click-bait” style title might be “How to minimize your child’s antibiotic exposure” rather than “Why you should think twice before giving your child antibiotics.”

    I agree with the underlying message here, but I hate to see parents fraught with fear because they once gave antibiotics for an ear infection years ago and are afraid they messed their child up for life. Or have parents not treating serious bacterial infections out of fear of antibiotics.

    There are certainly times when antibiotics are over prescribed, and your 5 steps to prevent their use are right on. But sometimes, even with excellent nutrition and sanitation, kids get bacterial infections. I personally have always done the “watch and wait 48 hours” thing with ear infections, and my kids up until this year never needed antibiotics. However, within the span of 2 weeks, both my 3 and 7 year old got ear infections from a bad virus (the original infection was viral but the fluid let a bacteria multiply as a secondary infection). The pain was so bad for each of them they were vomiting and dizzy. I took them each to the urgent care and both times the eardrum was about to rupture (in each child). I was happy to receive antibiotics for them in this case, to prevent damage from rupture as well as to start them feeling better (which happened in 24 hours each time after starting the antibiotics).

    We did a mega dose probiotic (double their normal dose of Klaire labs Therabiotic) plus Saccharomyces boulardii (a beneficial yeast) as well as kefir, yogurt, and fermented veggies during the course of the antibiotics and for 10 days after, before going back to their usual dose of probiotics.

    I do not think that they will be damaged for life, their gut flora will need time to repopulate, yes, but it’s not the end of the world.

    Let’s not overexaggerate the good that properly prescribed antibiotics for bacterial (not viral) infections in children can do in preventing worse morbidity than untreated bacterial infections can.

    • (This is 1978) When my first daughter was 2, she all of a sudden became tearful, pale and sick. It was bedtime so I may have given her some liquid Tylenol and put her to bed. She woke up in the middle of the night with liquid coming from her ear dripping down her face. Of course, I was horrified the next day to find out that her eardrum had burst. Actually, I was told this was not uncommon with children at all. She did have an infection and took a antibiotic (too long ago for me to remember which) and her ear healed nicely. We had a recheck with a hearing specialist. The only consequence that I ever saw might be a hearing sensitivity, but in likelihood that is from TMJ related issues which runs in my family with the women. Like all consequences of illness, some secondary issues become important, others fade away…I took a lot of antibiotics in my childhood in the 1950-60’s and see a direct connection now. I attempt to not take an antibiotic for several years at a time. I have tried to relay information to young mother’s but the medical industry has made doctors looks like gods and pills like gold. I pray that more parents will listen more, read more, and think more about what the medical and pharma industry have become and be more careful with their “gifts”…their children.

  6. When I was eight, I almost died of bacterial meningitis. I was put on a round of five different antibiotics for a month and a half. Though I lived, I noticed that was the turning point in my life of lower energy levels and more health problems. I’m grateful that the antibiotics saved my life, but I always wonder how different my quality of life would have been if I had never gotten sick.

    • It does make one wonder. I am glad you survived, but I sometimes think about the fact of when people are sooo sick and live, but then a compromised life often, if it was the right thing to put them through that kind of life. Of course, we love them and don’t want to lose them, however we do lose them in a sense and they have losses also. This is partly why I wonder if synthetic drugs are really good at all. Sometimes I wish we could go back to nature’s remedies exclusively but Americans in general would have a hard time with that compromise. And, if I had a sick child, I would be fraught with worry. My granddaughter at 2 months old caught Pertussis and if she hadn’t of had an antibiotic might have died. She is 15 now, but still has a cough and may have respiratory problems later. I still think breast-feeding has a lot to do with the primary protection of many diseases. Prayers for your health journey.

  7. Hi Chris, I really appreciate this article. I wish I had been educated about ear infections and antibiotics before I took my 9-month-old to the doctor in which he was prescribed Amoxicillin back in 2008. Unfortunately, he had a severe allergic reaction and was diagnosed within 3 weeks of his first dose with Autoimmune Hepatitis 2 (his immune system was destroying his liver). He went for a liver transplant but the system failed him and he passed away 30 days later. If I had only known, I would’ve done what we do now with our kids, colloidal silver in the ear and toughing it out for a day.

    So keep it up, my family truly appreciates this forward thinking and know that it can help avert tragedy!


    Corey Leamon

    • I have a friend who makes Colloidal Silver, has a machine, and takes it every day and never gets sick. I hope to learn more about it.

  8. My sons are 18 and 21. Both took antibiotics for severe ear infections when they were young. What can be done to bring their microbiome back to a healthy state? Can you point me to any articles? Thank you.

  9. My daughter had a course of amoxicillin for an ear infection when she was 2,5. Afterwards she got an eczema she has not been able to fully shake off since and she’s 4 now. We eat a real food diet with lots of broth, gluten-free, include prebiotics etc. but this is still very persistent. We have recently cut out dairy which so far seems to help.
    I was wondering if there is much difference between different types of antibiotics? What would be the worst type and what would be the ‘safest’ type to take if needed?

  10. The use of botanicals rather than antibiotics is common among the alternative medicine community and I am aware of many that are very effective. I’m wondering if there are studies on the effects of antibacterial botanicals on the gut flora. Do we know if the effects on the gut flora are not as negative (or perhaps they are even positive) as prescription medications?

  11. I wonder more about the COMBINATION of taking antibiotics AND consuming glyphosate contaminated foods at the same time. I’ve heard someone plant that seed, can’t recall who, but makes a lot of sense to me that the two together would be very distructive. Additionally, I know several children who have developed digestive related issues and have not had an antibiotic in their life… which leads me back to believing GLYPHOSATE alone to be more destructive than antibiotics alone. What are your thoughts on this idea Chris? Thanks for your time and interest researching and reporting!

  12. The American Heart Association prescribes amoxicillin for all dental work for people with certain conditions.
    How can one mitigate the impact of regular amoxicillin on the gut biome?

    • And dentists and docs disagree. Some will not work with you without the “preventative” dose. What are the options, besides finding a new dentist, to avoid that 1% chance (I have been told) of an infection from dental work?

    • I recently had major dental work (extraction of a root canaled tooth and two implants) and my holistic dentist prescribed a number of herbal antimicrobials including Colloidal Silver for a few days in place of antibiotics, followed with a course of black cumin oil.

      • I found that coconut oil, mixed with a blend of cinnamon bark essential oil, peppermint essential oil and clove essential oil, kept in the mouth for 10 mn several times a day, is much more effective than any antibiotics for the mouth.

      • Hi Evi, I am in search of a holistic dentist. Could you recommend a way to find one? Not sure which part of the country you live in. Thanks!

  13. I am facing the decision of whether or not to take antibiotics for a BV infection and I’m pregnant. My midwife of course is telling me to take the Metronidazole, citing risks of preterm labor, but I was hardly having any symptoms to begin. I am hesitant. Do you know of anyways of naturally curing a persistent BV infection or balancing the bacteria “down there”?

  14. What about strep throat? My kids have never been on antibiotics and my kids Doctor is supportive, unless they get strep throat. Is it possible to treat strep without antibiotics? She’s worried about it spreading to the heart.

    • Yes, again our holistic ped treated my son’s strep throat (scarlet fever to be more presice, which is a step infection) with homeopathic remedies.
      Interestingly, she used the same ones that I saw in Dr Cowan’s book (see my post below).
      I have also talked at the time with friends who are conventional doctors and informed me that the latest research shows that antibiotics do not stop strep’s side effects, though I do not have any reference for this. But they themselves did not give their son antibiotics for a strep throat.

  15. Is it possible that antibiotics, or dysbiosis in general is the cause of my son’s sudden (4 years ago following a round) pasty stool that takes a long time to clean? We’ve tried everything including fmt at a clinic, daily sauerkraut and probiotics. Should I be thinking away from bacteria now? Thank you

  16. This article comes at a very interesting time for me. My 6 yr old daughter was recently prescribed a low dose preventative antibiotic because she has reflux into her kidneys. She will be on it for a year! I was actually going to email and ask your thoughts on this. When I brought up all of the negative impacts that you mentioned to her doctors, she said only that possible dialysis down the road would be much worse. She has had 4 UTIs in 3 years, and her kidneys have no damage. I still think it’s drastic considering we’re doing several other things to prevent the UTIs.

    • My son had kidney reflux (2nd-3rd grade) and he was on antibiotics for 18 months since he was 3 months old. We found a good holistic pediatrician then and we stopped the antibiotics and took homeopathic remedies and Uva Ursi instead. It did wonders for us.

      • Ι have to add that these 18 months on antibiotics had a devastating effect on his microbiome and it took me three years on GAPS diet and homeopathic approach to help him find a balance.

    • You should try I Uva ursi and a biofilm disrupter!! I tried clearing it on my own for 2 months with lots of things and couldn’t shake it. My doc finally convinced me to take antibiotics for a uti and it came right back!! Then I discovered above I’ve been clear every since!!

    • You may want to have her cortisol level checked – recurring UTI’s can be a sign of low cortisol…

  17. My daughter was 11 and had a horrible bug. We watched and waited, and finally 3 weeks later (i think she got a secondary infection), we gave in and picked up the antibiotics that our doctor prescribed. I gave her probiotics along with it, as this was only her 3rd time taking antibiotics, and I knew how harsh they could be. Well, she got something called antibiotic induced, lactose intolerance, and when I say it was severe, I mean SEVERE. She could not have ANYTHING with even a hint of lactose. Come to find out the probiotics that I was giving her were lactose based (which usually dissipates during the process), and they made it even worse. We discovered how much of our food has some sort of, even minute amounts of dairy/lactose, even bacon (caramel coloring). We both learned so much, and I feared that her issues-massive belching for 5-8 hours on end, excruciating stomachaches, and fatigue would stay with her for her lifetime. We tried so many thing, antacids (big mistake-made it worse), HCL, and papaya enzymes both helped a bit, no dairy, no gluten, no processed foods probably helped to heal her gut, as well. The thing that has, literally, cured her is Prescript-Assist, soil based probiotics. Lifesaver doesn’t even begin to explain the change from this supplement.
    I am terrified of antibiotics now that I can see the damage they can wreak our on sensitive guts. I know I have a messed up biome that I passed on to my poor girlie, but Prescript-Assist has changed her life, thankfully.

    • i forgot to add that this lasted almost a full year before we saw a nutritionist who gave us the Prescript-Assist. It then took almost another year for her to be able to eat what she wants with no ill effects. So almost two full years of dealing with the affects of a 10 day course of antibiotics.

      (she knows to eat healthy now, as she doesnt ever want to go back to where she was, but it’s nice that she can have a cupcake at a birthday party, or bacon at a friend’s house).

  18. Great article!

    I have asthma + sinusitis that developed in adulthood. Not sure what the cause is, but I’m sure it didn’t help that I was on antibiotics 3x per year, at least until I was 20. I know it’s hard when colds and sinus infections last weeks and we all wish there was a quick fix – it’s just not worth it.

    I would also love to see how this research correlates with having been breastfed or not.

  19. Thanks so much for this post. When my daughter was two, she came down with a case of bacterial pneumonia and HAD to be treated with antibiotics (and a freaking lot of them, I’m sorry to say). This was one of those diseases that kids died from thirty-forty years ago.

    I agonized after the treatment was over because she was getting sick so often… she’s eight now and it’s only been about a year since she stopped coming down with every bug that crossed her path. These issues are such an important thing to get across to people.

    Yes, in this case, her life was absolutely saved by antibiotics. The point is that the treatment was not without its problems for years afterward.

    • Yes, often it’s not a black & white. We may have to use the antibiotics, but they’re not without cost. So the idea is to do whatever we can to reduce the need for them first of all, and then take steps to mitigate their effects when we have to take them.

    • My daughter at age 1.5 came down with a severe case of pneumonia. My holistic paediatrician and we, her parents, decided not to use antibiotics although it was agonizing seeing my baby perishing.
      The paediatrician prescribed black mustard compresses which apparently are very potent in treating chest infections, along with a couple of anthroposophic tinctures. The result was miraculous!
      I was later very happy to see that Dr. Cowan also prescribes mustard compresses for chest infections in his book with Sally Fallon, The Nourishing Traditions Book of Baby & Child Care.
      I had my daughter on the GAPS diet for a about a year after the pneumonia, and now she is 5.5 and thriving, she rarely gets sick any more except for the occasional sniffles.
      Perhaps I should add that she was never vaccinated so her immune system was in a pretty good shape to handle the infection.