Medically reviewed by Jonathan Hansen, MD, PhD

Antibiotics are not a go-to drug for the treatment of IBD, but they can be useful in certain circumstances. For instance, antibiotics are typically very effective at treating infectious diarrhea and also anal fistula drainage. In these cases, the benefits of relief of symptoms usually far outweighs the risk of side effects.

This primer will help you get up-to-speed on the basics of antibiotics and what they’re used for with IBD. You’ll find more info on commonly prescribed antibiotics for IBD and on possible long-term effects, such as becoming more susceptible to harmful bacteria, in a couple of related articles.

Common IBD-Related Uses of Antibiotics

1. Abscesses or Fistulas.

Antibiotics are frequently prescribed to patients with Crohn’s disease who have abscesses or fistulas, which are caused by bacteria. The antibiotic helps by reducing the quantity of bacteria in the fistulas and abscesses, and therefore the amount of fistula drainage and number of abscesses.

2.  Post-Surgery.

Doctors also may prescribe antibiotics such as metronidazole (Flagyl) after surgery in Crohn’s disease to help prevent its recurrence. In patients who have had their UC treated by surgical removal of the colon and creation of a J-pouch, doctors often prescribe antibiotics such as metronidazole or ciprofloxacin if the J-pouch becomes inflamed (called pouchitis).

3. Infection.

Antibiotics are also prescribed as a treatment for disease-related infections in the intestine, which can manifest the same symptoms as a flare-up of IBD itself. In this situation, your doctor will most likely take a stool sample to determine if you have an infection, then decide whether or not to prescribe antibiotics.

The most commonly diagnosed intestinal infection in IBD patients is Clostridium difficile, as shown in the above image. This “bad” bacteria, sometimes called C. diff, causes disease when the “good” bacteria in the gastrointestinal tract are killed off. This infection is becoming increasingly common, and IBD patients tend to be more prone to it. Ironically, the method for treating a Clostridium difficile infection—antibiotics—is also often the reason why it occurs in the first place: The antibiotics that are given to treat another issue have killed off too many of the beneficial bacteria in the intestine, allowing the C. diff to take hold. Most antibiotics can cause this specific infection; only a select few, such as metronidazole, can eliminate it.

4. General Inflammation.

Even when tests for infection come back negative, doctors occasionally will prescribe antibiotics to manage inflammation or other flare symptoms you might be experiencing. This is not a common practice and there is not much scientific evidence to support it, but some researchers believe that antibiotics can control IBD symptoms by reducing bacteria in the intestine overall, which reduces the overactive drive of the immune system in the intestine.

Keep Your Doctor Informed

While you might find yourself grateful for an antibiotic prescription to help control symptoms associated with IBD—or for its use in the process of maintaining remission of IBD symptoms—keep in mind that antibiotics should be used under the supervision of your doctor, and with careful consideration of their potential side effects (both in yourself as well as an unborn child, should you take them during pregnancy).


Tara Baukus Mello

With more than 4,000 articles to her credit, Tara Baukus Mello’s work has appeared in such publications as Woman’s Day, The New York Times, The Los Angeles Times, and cNet.com, among others.

Medical reviewer and Oshi physician-partner Jonathan Hansen, MD, PhD, has been involved in 20-plus clinical trials of investigational compounds that target various pathways important in the development of IBD. He has co-authored book chapters on IBD and been published in a variety of peer-reviewed journals, and his interests include the role of environmental bacteria in the development of chronic intestinal inflammation. Dr. Hansen serves as an Associate Professor of Medicine in the Division of Gastroenterology & Hepatology at the University of North Carolina at Chapel Hill. He received his BS in Biochemistry from Brigham Young University, and his MD and PhD in Microbiology and Immunology from Indiana University School of Medicine.

Oshi is a tracking tool and content resource. It does not render medical advice or services, and it is not intended to diagnose, treat, cure, or prevent any disease. You should always review this information with your healthcare professionals.