Common and Serious Antibiotic Side Effects in Children

Like any medications you or your child receive, antibiotics can come with side effects. Most often, the benefit of these drugs far outweigh any risks, but adverse reactions do occur. Learn about the common and less common side effects of antibiotics and how you can reduce the risks.

Mother Giving Penicillin Medicine to His Sick baby Boy
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Antibiotics for Childhood Infections

Although antibiotic use has gone down in the past 10 to 20 years, they are still some of the most prescribed medications in pediatrics.

Contributing to the drop in antibiotic prescriptions include:

  • The addition of Prevnar to the childhood immunization schedule, which has directly led to fewer ear infections
  • More widespread use of the flu vaccine, which can lead to fewer kids with flu and secondary ear infections
  • More awareness of the risks of antibiotic resistance, such as from MRSA
  • Better antibiotic prescribing guidelines, including guidelines that advocate for watchful waiting for some kids with ear infections and sinus infections

Most importantly, though, there is a greater understanding of antibiotic side effects. Being aware of the side effects that antibiotics can cause will hopefully lead to even fewer unnecessary antibiotic prescriptions for colds and other viral infections so that antibiotics will work when we need them.

Your chances of a side effect from an antibiotic severe enough to send you to the emergency room are 1 in 1000, while the chances that an antibiotic actually help prevent a serious complication of an upper respiratory infection are four times less (1 in 4000).

Common Side Effects

If your child develops a side effect while taking, or immediately after stopping an antibiotic, be sure to tell your pediatrician. Common antibiotic side effects can include the following.

Antibiotic-Associated Diarrhea

Getting diarrhea when you take an antibiotic is much more common than many parents understand. It is thought that up to 25% of children will develop diarrhea, either while they are still taking the antibiotic, or up to a few weeks after they have finished it.

While some antibiotics are thought to be more likely to cause diarrhea, including Augmentin and erythromycin, just about any antibiotic can cause your child to have diarrhea.

Allergic Reactions

Antibiotics can commonly cause allergic reactions with hives. Unfortunately, many viral reactions can cause skin rashes that might be confused with an allergic reaction if they child is unnecessarily prescribed an antibiotic, causing problems when the child really needs the antibiotic at a later time.

Drug Reactions

Rashes as a drug reaction (rather than an allergic reaction) to an antibiotic may include itchy, maculopapular rashes or even delayed-onset urticarial (look like hives) rashes, but which is not an IgE-mediated allergic reaction and so won't cause life-threatening anaphylactic reactions.

Yeast Infections

Yeast infections may occur in different regions of the body and may include oral rashes (thrush) or genital rashes (Candidal vulvovaginitis).

Stained Teeth

Classically, tetracycline derivatives caused tooth staining when given to young children during periods of enamel calcification, which is why these antibiotics (tetracycline, doxycycline, and minocycline) are not routinely used in children under the age of 8 years.

Surprisingly, it is thought that even Amoxil may cause stained teeth. One study reported that kids who took Amoxil in the first three to six months of life had an increased risk of tooth staining later.


Although often overlooked as a side effect, some antibiotics have been associated with a drug-induced fever when they are given intravenously (by IV).

Most of these side effects are temporary, are not life-threatening, and go away once your child finishes taking the antibiotic. Allergic reactions may need to be treated with antihistamines or corticosteroids, and yeast infections may need to be treated with topical antifungal medications.

Serious Side Effects

Antibiotics don't just cause diarrhea and rashes. Based on 2013-2014 data, there were four adverse-drug-related emergency room visits for every 1000 individuals annually. Among children, antibiotics were the most common reason for the visit.

Children under the age of 5 years have one of the highest rates of emergency room visits involving medication side effects. That's not surprising when you consider that some of those more serious side effects can include:

  • Anaphylaxis: Anaphylaxis is a life-threatening allergic reaction that includes multiple allergy symptoms, especially trouble breathing and/or reduced blood pressure.
  • Stevens-Johnson syndrome: This is a life-threatening hypersensitivity reaction. Children with Stevens-Johnson syndrome develop flu-like symptoms with painful ulcers or erosions in the mouth, nose, eyes, and genital mucosa, often with crusting.
  • Toxic epidermal necrolysis (TEN): This is a severe form of Stevens-Johnson syndrome.
  • Musculoskeletal problems: Cipro (ciprofloxacin) and other fluoroquinolones are not generally used in children. They carry a risk of tendon rupture and possibly permanent nerve damage, especially in children, Cipro can cause bone, joint, and tendon problems, including pain or swelling.
  • Clostridium difficile infections: This bacteria can cause diarrhea and other gastrointestinal symptoms. It is especially common in children who have recently been on antibiotics.
  • Red man syndrome: A reaction that may occur in children who are getting IV vancomycin, red man syndrome includes flushing of the head and neck and sometimes, more seriously, life-threatening reactions.
  • Ototoxicity: Some antibiotics, especially aminoglycosides (gentamicin), can cause cochlear or vestibular damage, leading to hearing loss. It is important to monitor drug levels when children, especially newborns, are given this antibiotic for a severe infection.
  • Pill esophagitis: A child's esophagus can be irritated by an antibiotic pill he is taking, especially if he has been prescribed doxycycline, which is rather large.
  • Photosensitivity: Many antibiotics, especially those used to treat acne, can make children more sensitive to the sun. This includes the antibiotics, tetracycline, minocycline, and doxycycline, for which extra care to reduce sun exposure should be taken while your teen is taking them.
  • Drug-induced lupus: Children can develop symptoms of systemic lupus erythematosus (SLE) while taking certain medications, especially high doses of minocycline for long periods of time.
  • Idiopathic intracranial hypertension: Minocycline can sometimes cause intracranial hypertension or pseudotumor cerebri, in which children taking the medicine develop a chronic headache, nausea, and vomiting.

Antibiotics are responsible for 56% of emergency room visits by children age 5 and younger who are having an adverse drug event.

Avoiding Side Effects

The best way to avoid antibiotic side effects is to only get a prescription for an antibiotic when it is needed to treat a bacterial infection and take to take it as it is prescribed.

In addition to encouraging antibiotic resistance (when antibiotics can't kill bacteria anymore), taking antibiotics when they aren't needed can put your child at risk for side effects. A prescription for Amoxil or Zithromax can't cause diarrhea or an allergic reaction if it was never written in the first place.

But when antibiotics are needed, like when your child has strep throat or pneumonia, you might be able to avoid or at least reduce your child's chance of developing side effects by doing the following:

  • Take a probiotic. Several studies have shown that probiotics can prevent antibiotic-associated diarrhea in children.
  • To prevent pill esophagitis, have your child drink a full glass of water if taking doxycycline or other large pills or capsules.
  • Being extra careful to protect your child from the sun if taking an antibiotic that might put themat increased risk for sunburn. Use sunscreen, dress in protective clothing, and limit exposure to the sun when it is at its strongest.
  • Take the antibiotic as prescribed, including finishing the whole prescription so that you don't have any leftover medicine.
  • Avoid interactions with other medications by making sure your pediatrician knows about all other medications, including over-the-counter and natural remedies, that your child may be taking.
  • Store the antibiotic properly, especially if it needs to be refrigerated.
  • Follow directions on whether or not to take the antibiotic with food or on an empty stomach.

Most importantly, though, review the latest antibiotic prescribing guidelines so that you aren't looking for an antibiotic every time your child has a runny nose, sore throat, or minor ear infection.

What Else to Know

Although sometimes just a nuisance, side effects from antibiotics can be serious. Other things to know about antibiotic side effects include that:

  • Although not commonly used to treat young children, Doxycycline is indicated for children with ehrlichiosis and Rocky Mountain spotted fever, even if they are under age 8. In these cases, the risks of these serious tick-borne diseases are outweighed by the risks of taking the antibiotic.
  • In children, Cipro is indicated for the treatment of complicated urinary tract infections and pyelonephritis (kidney infection) due to Escherichia coli. It is not, however, a first choice drug in young children.
  • Omnicef (cefdinir) can sometimes cause a child's stool to have a reddish color because of an interaction with iron vitamins, baby formula with iron, or other iron-containing products.
  • Amoxil (amoxicillin) sometimes causes behavioral changes, including hyperactivity and agitation.
  • Children with a glucose-6-phosphatase deficiency (G6PD deficiency) should not take certain antibiotics because of the risk of developing hemolytic anemia. Examples of these antibiotics include sulfonamides and nitrofurantoin.

A Word From Verywell

Antibiotics treat life-threatening infections and have been described as miracle drugs and as one of the 10 great public health achievements of the 20th century. Don't let worry of side effects keep you from taking antibiotics when you need them.

If your child does have a serious side effect that is associated with taking an antibiotic, you can report it to the FDA through their MedWatch online voluntary reporting form.

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Article Sources
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Additional Reading
  • Zareifopoulos N, Panayiotakopoulos G. Neuropsychiatric effects of antimicrobial agents. Clinical Drug Investigation. 2017;37(5):423-437. doi:10.1007/s40261-017-0498-z

  • Kliegman, Robert M., Bonita Stanton, St Geme III Joseph W., Nina Felice. Schor, Richard E. Behrman, and Waldo E. Nelson. Nelson Textbook of Pediatrics. 20th Edition. Philadelphia, PA: Elsevier, 2015. Print.