For people with Crohn’s, antibiotics may help lower the amount and change the composition of bacteria in the intestines, which may relieve symptoms. They can also treat infections.

Antibiotics may help reduce certain bacteria in the intestines in people with Crohn’s disease. They also work to treat infections, such as those that occur with complications like abscesses and fistulas.

Antibiotics can target bacteria broadly or target more specific types of bacteria. The type of antibiotic you need can depend on where an infection is located in the body. If one type of antibiotic doesn’t work or causes bothersome side effects, a doctor may prescribe a different one.

Some infections that may require antibiotic therapy include:

  • Clostridium difficile (C. diff)
  • Giardia lamblia
  • Escherichia coli (E. coli)

Keep reading to learn about different antibiotics used to manage Crohn’s disease and its complications and the side effects to watch out for.

Several antibiotic medications can be useful in Crohn’s disease, both to treat the disease itself and its complications, such as abscesses and fistulas.

Abscesses are small pockets of infection, and they can contain fluid, dead tissue, and bacteria. Fistulas are unusual connections between your intestines and other body parts, or between two loops of your intestines. Abscesses and fistulas occur when your bowels are inflamed or injured.

Fistulas can affect up to half of people with Crohn’s within 20 years of diagnosis and cause abscesses to form. Abscesses often need to be drained through surgical procedures.

Doctors typically prescribe antibiotics to help resolve these infections. Antibiotics for Crohn’s disease can include:

Doctors may prescribe ciprofloxacin (Cipro) to treat infections in people with Crohn’s disease. When taking ciprofloxacin, it’s important to maintain consistent medication levels in the bloodstream during treatment, so try not to miss any doses.

Ciprofloxacin treats a wide spectrum of bacteria both inside and outside the intestines.

Tendon rupture can be a side effect, although this is rare. Other possible side effects include nausea, vomiting, diarrhea, and abdominal pain.

Used alone or in combination with ciprofloxacin, metronidazole (Flagyl) is commonly used to treat complications such as abscesses and fistulas. It may also help reduce disease activity and prevent recurrence. Like ciprofloxacin, it also treats a wider range of bacteria in the digestive tract.

Side effects of metronidazole may include numbness and tingling in your extremities, and muscle pain or weakness.

It’s important to be aware that drinking alcohol while taking metronidazole may also cause side effects. Nausea and vomiting may occur, as well as an irregular heart rate in rare instances. Make sure to contact your doctor if you experience any of these symptoms.

Doctors often prescribe rifaximin (Xifaxan) to treat diarrhea. Rifaximin only acts on bacteria in the intestines, so it may not disrupt other bacteria in the body the way certain other antibiotics might.

However, rifaximin may also help induce or maintain Crohn’s remission, though a 2024 review of research noted that it may not be as effective as other antibiotics for this purpose. However, additional research is still needed.

Possible side effects may include:

  • skin rash or hives
  • bloody urine or diarrhea
  • fever

Rifaximin may also be costly, so it’s important to ensure your insurance covers it before picking up your prescription.

Ampicillin is another medication that may help treat infections that can occur with Crohn’s disease, such as abscesses and fistulas. This drug is in the same family as penicillin and usually takes effect within 24 to 48 hours.

Side effects may include:

  • diarrhea
  • nausea
  • rashes
  • inflammation and redness of the tongue

Doctors prescribe tetracycline for a variety of infections, including traveler’s diarrhea. It also inhibits bacteria growth.

Possible side effects of tetracycline include:

Amoxicillin is another antibiotic in the penicillin family. It can act on bacteria both inside and outside the intestines.

It’s not often used for Crohn’s disease specifically and usually targets respiratory infections and Helicobacter pylori (H. pylori) infections. H. pylori is a bacteria associated with the development of stomach ulcers.

It’s generally safe to take if you have Crohn’s disease as long as you follow a doctor’s instructions. However, amoxicillin can cause gastrointestinal side effects like:

  • nausea
  • vomiting
  • diarrhea

Antibiotics may help control your symptoms, but they may not affect the progression of Crohn’s disease. In some cases, people stop taking antibiotics when they feel the side effects of the medication may be more severe than Crohn’s symptoms.

Remember, everyone responds to treatment differently. Be sure to discuss your options with your doctor to find out if antibiotics may be effective for you.