Medically reviewed by Jonathan Hansen, MD, PhD

If you’re like so many of us, you’ve got an antibiotics prescription in one hand and a bunch of questions in the other, so here’s a look at the most commonly prescribed antibiotics for IBD.

While it’s possible for your doctor to prescribe any one of the more than 100 antibiotics available today to treat IBD-related infections or symptoms of flare-ups, there are four antibiotics that are most commonly prescribed for people with IBD:

    • Metronidazole (Flagyl)
    • Ciprofloxacin (Cipro)
    • Vancomycin (Vancocin)
    • Rifaximin (Xifaxan)

These four are usually swallowed in pill form, though two of them can also be administered via shots or intravenously. As with any antibiotic, the entire prescription should be taken exactly as directed, even if you feel better. If your symptoms are not gone by the time the prescription is completed, talk to your doctor.

Overall, most people experience no side effects from antibiotics, though sometimes they can cause such symptoms as nausea, vomiting, appetite loss, rash, diarrhea, dizziness, and headaches. Definitely contact your doctor if you have particularly bothersome side effects.

As with taking any medication, you should ask your doctor or pharmacist if there are any interactions with your current medications, including supplements and over-the-counter, alternative, and homeopathic remedies. People who take the blood-thinning anticoagulant warfarin, also known by the brand name Coumadin, need to be particularly cautious when taking antibiotics, as they can interact dangerously.

Here’s a breakdown of all you need to know about the four most common antibiotics prescribed for IBD infections or symptoms.

Metronidazole (Flagyl)
Drug Class: Nitroimidazoles

What It’s Used For: A broad-spectrum antibiotic designed to fight a wide range of bacteria both inside and outside the intestines. Typically used with or without ciprofloxacin in people who have Crohn’s disease to reduce fistula drainage from around the anus, as well as to treat Clostridium difficile infection.

Possible Side Effects: Dark or reddish-brown urine and a metallic taste in the mouth, neither of which are serious. People taking metronidazole long-term may experience tingling in the hands and feet, which can continue even after the drug is stopped, so notify your doctor at the first signs of tingling. Prolonged use can also result in an oral or vaginal fungal infection, so tell your doctor if you develop white patches in your mouth or experience a change in vaginal discharge.

Possible Interactions: Alcohol should be avoided while taking this medicine and for at least two days after the last dose, because metronidazole affects the breakdown of alcohol and can result in nausea and vomiting.

Ciprofloxacin (Cipro)
Drug Class: Fluoroquinolones

What It’s Used For: A broad-spectrum antibiotic used to treat an array of bacteria inside and outside the intestines. Typically used with or without metronidazole in patients with Crohn’s disease to reduce fistula drainage from around the anus.

Possible Side Effects: This drug can make the skin very sensitive to the sun. People taking it should wear sunscreen, limit sun exposure overall, and avoid tanning booths. With long-term use, people taking this drug may experience tendonitis, especially of the Achilles tendon, even resulting in rupture, though this is considered rare. Ciprofloxacin also can sometimes cause diarrhea, either directly by disturbing the normal bacteria that live in the colon or indirectly by creating conditions that result in a Clostridium difficile infection.

Possible Interactions: Ciprofloxacin can interact with antacids, such as Tums and Rolaids, as well as vitamins and mineral supplements containing calcium, iron, or zinc, all of which make ciprofloxacin less effective. It is generally not prescribed for those under age 18 because it can cause problems with bones, joints, and the tissue surrounding joints in children.

Vancomycin (Vancocin)
Drug Class: Glycopeptides

What It’s Used For: The oral form of vancomycin is used to specifically to treat Clostridium difficile infections of the colon. It focuses only on the intestines and will not kill bacteria or treat infection in other parts of the body.

Possible Side Effects: Nausea and vomiting are rare side effects.

Possible Interactions: Since this drug is not absorbed into the bloodstream, there are very few drug interactions, but it is always good to check with your doctor or pharmacist.

Rifaximin (Xifaxan)
Drug Class: Glycopeptides

What It’s Used For: Rifaximin is used to treat infection specifically in the intestines known as traveler’s diarrhea. Since very little of this drug is absorbed into the bloodstream, it won’t kill bacteria or treat infections in other parts of the body.

Possible Side Effects: Side effects are uncommon, but can include pain in the joints and tightening of the muscles, as well as excessive tiredness.

Possible Interactions: Rifaximin can sometimes cause excessive growth of “bad” bacteria, resulting in a Clostridium difficile infection, though this is less common than with most antibiotics.


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.