For people with celiac disease, sticking to a strict gluten-free diet isn’t just a recommendation-it’s life-saving. But even when you avoid bread, pasta, and beer, some patients still struggle with bloating, diarrhea, and abdominal pain. Why? Because celiac disease doesn’t always clean up after itself. In many cases, the damage to the small intestine creates the perfect environment for bacteria to overgrow, leading to a condition called small intestinal bacterial overgrowth, or SIBO. That’s where rifaximin comes in.
What is rifaximin and how does it work?
Rifaximin is an antibiotic that works almost entirely inside the gut. Unlike other antibiotics that get absorbed into your bloodstream and affect your whole body, rifaximin stays in the intestines. It doesn’t get absorbed much at all-less than 0.4% enters your blood. That means it targets harmful bacteria in your small intestine without wiping out good bacteria elsewhere or causing widespread side effects.
It’s not a cure for celiac disease. You still need to avoid gluten. But rifaximin helps clear out the extra bacteria that thrive in the damaged lining of the gut. These bacteria ferment undigested food, produce gas, and irritate the gut wall. When they’re reduced, symptoms like bloating, diarrhea, and cramping often improve significantly.
Studies show that in patients with celiac disease who still have symptoms despite following a gluten-free diet, rifaximin reduces SIBO in about 70% of cases. One 2022 trial published in Clinical Gastroenterology and Hepatology found that after a 10-day course of 550 mg rifaximin three times a day, 68% of participants tested negative for SIBO on breath tests. Their symptoms dropped by over 50% within two weeks.
Why do people with celiac disease get bacterial overgrowth?
The small intestine is designed to absorb nutrients, not host large amounts of bacteria. In healthy people, the gut moves food along quickly, and stomach acid and bile keep bacterial numbers low. But in celiac disease, the immune system attacks the villi-tiny finger-like projections in the small intestine that absorb nutrients. When these villi flatten out from damage, food moves slower, digestion becomes inefficient, and undigested carbs pile up.
That’s like leaving a bowl of sugar out in the open. Bacteria feast on it, multiply, and start producing hydrogen and methane gas. That’s what causes the bloating, the urgent diarrhea, and the feeling that your stomach is a balloon you can’t pop.
Even after going gluten-free, it can take months-or sometimes years-for the gut to heal completely. During that time, the environment stays ripe for overgrowth. That’s why some people stay symptomatic even on a perfect diet. Rifaximin breaks that cycle.
How is rifaximin different from other antibiotics?
Most antibiotics, like amoxicillin or doxycycline, travel through your bloodstream. They can kill good bacteria in your colon, leading to yeast infections, diarrhea, or even long-term microbiome disruption. Rifaximin doesn’t do that.
Because it’s not absorbed, it doesn’t interfere with your liver, kidneys, or other organs. It also doesn’t increase the risk of antibiotic resistance in your body’s normal flora. That’s a big deal. In a 2023 review in Gut Microbes, researchers noted that rifaximin had the lowest rate of resistance development among gut-targeted antibiotics over a five-year period.
It’s also taken orally, in pill form, and usually for just 10 to 14 days. No injections. No hospital visits. No long-term use. That makes it practical and safe for repeat use if symptoms return.
Who should consider rifaximin for celiac disease?
If you’ve been gluten-free for at least six months and still have:
- Chronic bloating or distension
- Diarrhea that won’t go away
- Excessive gas or burping
- Abdominal pain after eating
- Fatigue or brain fog despite eating well
Then you might have SIBO. The first step is a breath test-either hydrogen or methane. These tests are non-invasive. You drink a sugar solution, then breathe into a tube every 15 minutes for two to three hours. The machine measures gases your gut bacteria produce.
If the test is positive, rifaximin is often the first-line treatment. It’s not for everyone. If you’ve had repeated courses of antibiotics in the past, or if you’re immunocompromised, your doctor may look at other options. But for most people with persistent celiac symptoms, it’s the most targeted, safest choice.
What to expect during and after treatment
Most people take rifaximin three times a day for 10 to 14 days. Side effects are rare. The most common is mild headache or dizziness-less than 5% of users. You won’t get yeast infections or severe diarrhea like with other antibiotics.
Many patients notice improvement within 3 to 5 days. Bloating drops. Stools firm up. Energy returns. But it’s not magic. You still need to eat a clean, low-fermentable diet during and after treatment. That means avoiding high-FODMAP foods like onions, garlic, apples, and beans for a few weeks. These foods feed bacteria, and if you eat them too soon, the overgrowth can come back.
Some people need a second course six months later. That’s normal. Healing the gut takes time. Rifaximin gives you a reset button-not a permanent fix.
Can rifaximin replace a gluten-free diet?
No. Never. This is critical.
Rifaximin treats the side effect-not the cause. Celiac disease is an autoimmune condition triggered by gluten. If you go back to eating wheat, barley, or rye, your immune system will attack your gut again. The villi will flatten. Bacteria will return. Rifaximin will only work temporarily.
Think of it like cleaning a clogged sink. Rifaximin unclogs it. But if you keep pouring grease down the drain, it will clog again. Gluten is that grease.
Always pair rifaximin with strict gluten avoidance. And consider working with a dietitian who specializes in celiac disease. They can help you identify hidden sources of gluten and suggest low-FODMAP, nutrient-dense foods that support healing.
Are there alternatives to rifaximin?
Yes-but none are as well-studied or as targeted for celiac-related SIBO.
Neomycin and metronidazole are sometimes used, but they’re absorbed into the bloodstream and carry higher risks of nerve damage, yeast infections, and resistance. They’re not first-line.
Probiotics like Saccharomyces boulardii or Lactobacillus strains can help restore balance after antibiotics, but they don’t kill off overgrown bacteria on their own.
Dietary changes-like a low-FODMAP or elemental diet-can reduce symptoms, but they’re hard to follow long-term and don’t address the bacterial overgrowth directly.
Rifaximin remains the gold standard for treating SIBO in celiac patients because it’s effective, safe, and doesn’t disrupt the rest of your body.
Real patient outcomes
In a clinic in Cape Town, a 34-year-old woman came in with six months of bloating and fatigue. She ate only gluten-free food-no cheat days. Her blood tests showed healed antibodies. But her breath test was positive for hydrogen-dominant SIBO. After 10 days of rifaximin, she reported a 70% drop in bloating. Her energy returned. She started walking again. She didn’t need to change her diet further. Just the antibiotic made the difference.
Another patient, a 52-year-old man with long-standing celiac disease, had tried everything: enzymes, probiotics, elimination diets. Nothing worked. After rifaximin, his diarrhea stopped. He gained 5 pounds of muscle mass because his body could finally absorb protein again.
These aren’t rare cases. They’re common.
When to talk to your doctor
If you have celiac disease and still feel unwell after six months on a gluten-free diet, don’t assume it’s just ‘hard to heal.’ Ask for a breath test. Ask about SIBO. Ask about rifaximin.
Many doctors still don’t know about the link between celiac disease and bacterial overgrowth. But the evidence is growing. In 2024, the European Society for the Study of Small Intestinal Bacterial Overgrowth updated its guidelines to include rifaximin as a recommended treatment for celiac patients with persistent symptoms.
Don’t suffer in silence. Your gut can heal. But sometimes, it needs a little help to get back on track.
Can rifaximin cure celiac disease?
No, rifaximin cannot cure celiac disease. It only treats bacterial overgrowth (SIBO), which is a common secondary condition in people with celiac disease. The only treatment for celiac disease is a lifelong strict gluten-free diet. Rifaximin helps manage symptoms but does not stop the immune system from reacting to gluten.
How long does it take for rifaximin to work for celiac symptoms?
Most patients notice improvement in bloating and diarrhea within 3 to 7 days of starting rifaximin. Full symptom relief usually occurs by the end of the 10- to 14-day course. However, gut healing takes longer, and symptoms may return if the underlying causes-like poor diet or slow gut motility-are not addressed.
Is rifaximin safe to take more than once?
Yes, rifaximin can be safely repeated if symptoms return. Unlike many antibiotics, it doesn’t cause significant disruption to the gut microbiome or increase resistance risk. Studies show that up to two courses per year are well-tolerated in patients with recurrent SIBO. Always consult your doctor before repeating treatment.
Do I need a prescription for rifaximin?
Yes, rifaximin is a prescription-only medication in most countries, including South Africa, the U.S., and the EU. It is not available over the counter. You’ll need a diagnosis of SIBO-usually confirmed by a breath test-before your doctor will prescribe it.
Can I take rifaximin while on a gluten-free diet?
Yes, rifaximin is safe and effective to take while following a gluten-free diet. In fact, it’s most effective when combined with strict gluten avoidance. The antibiotic targets bacterial overgrowth, while the gluten-free diet prevents further immune damage to the gut lining.
Are there natural alternatives to rifaximin for SIBO?
Some people use herbal antimicrobials like oregano oil, berberine, or garlic extract to manage SIBO. While some small studies show promise, none have been proven as effective as rifaximin in clinical trials for celiac patients. Herbal options may help with mild cases, but for persistent or severe symptoms, rifaximin remains the most reliable choice.