I always thought rotating Cipro and flagyl meant alternating one or the other, not both, for a course of treatment. That’s what I’ve previously been prescribed for pouchitis....and only for two weeks. I’ve just been prescribed both for a month. One is twice/day, the other three/day. Is this what rotating typically means? Is taking both a common protocol?

Also, I’m a bit confused about dairy in foods being ok, but not to be taken with Cipro. Does this mean I need to give up goats milk kefir for now? Or do I try and time it hours apart from the Cipro? I consume 8 oz twice/day as part of my probiotics regimen. I hate to sacrifice the kefir which I think has been helpful, but I don’t want to decrease the Cipro efficacy either. 

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Rotating Cipro and Flagyl *does* mean alternating them. Combination therapy (taking both at once) should be reserved for special circumstances, such as when either drug alone has proven ineffective. I’m on both, and they work great for me, but I only do this because they no longer work individually. Taking both at once can make it hard to figure out what to do if a troubling side effect occurs.

Cipro just has to be separated from dairy by a few hours. Through experimentation I found that my (fairly low) Cipro dose works just as well once daily as when it’s split into two doses. I take it at bedtime, well separated from my yogurt/VSL mixture.

Is this a new doctor for you? Have your symptoms gotten worse or changed?  Is there any reason a more aggressive approach might be needed?

Thanks, Scott. This doctor isn’t new to me and is supposedly very experienced. 

The short answer is the symptoms I can feel haven’t worsened; I’ve greatly improved. But the doctor has been hesitant to prescribe antibiotics so I have only had them 2-3 times since 2013. 

I was treated in 2013 for pouchitis for the first time following an endoscopy. I had a second treatment in 2014 based on reported symptoms, no scope. In 2016 I complained of symptoms, had an endoscopy and was told it wasn’t pouchitis, no treatment. More tests due to suspected crohns, but was ruled out after a small bowel series and diet improved symptoms. This year everything looks and feels better, with the exception of chronic pouch inflammation and some new pouch ulceration. 

By 2013 I had suffered untreated for 13 years, found this doctor and within 24 hours on antibiotics I felt amazing. Just prior to that treatment, the symptoms finally brought me to my knees. I’ve never been in that bad of shape since, but it’s certainly been lingering with little treatment to the point it’s definitely affecting quality of life. I think I’ve gotten used to symptoms as though that’s just how it is, especially after continually receiving little treatment. 

It is confusing since I know I respond well to antibiotics. I think the ulceration is what has her concerned at this point and she’s not necessarily convinced it’s chronic pouchitis. 

If you are well (symptom-free) between treatments then it’s not *chronic* pouchitis. It’s just pouchitis. That ugly history was *untreated* pouchitis rather than what’s usually called “chronic pouchitis,” though it was chronic in the sense of lasting forever. It sounds like things looked pretty ugly inside at your last scope, so your doc decided to treat it more aggressively. The advantage of this is that it maximizes the likelihood of really clearing things up...if you can tolerate the medications.

I don’t know what probiotic dose you’re on, but a high dose seems to be more effective in preventing/delaying pouchitis recurrences. I take a maximum VSL dose (4 DS packets daily), but it’s very expensive. Fortunately I persuaded my insurance company to cover it, but I reach my out-of-pocket maximum every year.

I take both and rotate them with other antibiotics. You may find that when you stop taking them the pouchitis will return. If you keep going back to cipro and flagyl without rotating or stay on it for a long period of time, that’s when problems could develop, the most notable being yeast infections and possible skin issues like warts. Just play it by ear and do what you have to do. I take cipro and flagyl together mainly because they work better than if taken alone but would still rotate (IF you have to go back to antibiotics at some point) with tinidazole or xifaxin or both.

They wanted to use a different antibiotic for long term use (I don’t recall the name), but my insurance doesn’t cover it. 

It’s weird.....I haven’t gone all day and feel like I did before UC. No constipathon, no bloat, nothing. I was at at least 10 BM/day before all the changes I made on my own. With those changes I was down to 4-5 times. Yesterday was two times and nothing today. I could go, but I have no need. I’ve been on the antibiotics only 48 hours.

There’s really no reason to assume or expect that pouchitis will promptly recur when the antibiotics are stopped. That’s what happens to CT and me, but not what happens to most people.

The antibiotic with the best side-effect profile is Xifaxan (rifaximin). It’s very expensive, though. It works well for some folks, but didn’t do a thing for me. I’d guess that’s the most likely one that they’d prefer to use long-term. When insurance companies don’t like a medication you can sometimes get it covered by going through their appeal process. It takes patience and a supportive doctor, though.

Antibiotics have a constipating effect, particularly cipro and flagyl. This can be counteracted by keeping hydrated, eating fiber and natural laxatives, and avoiding Imodium and other thickening agents. Of all the antibiotics I take the cipro/flagyl has the most constipating effect but I can counteract as needed.

I thought I’d have to take Cipro and flagyl for a month, but it’s going to be two months followed by an endoscopy to see how things look. Then maybe taper or change to Rifaximin depending on how things look.

 I feel no symptoms and felt done before the Rx, though I definitely feel better with the Rx.

The Rx duration is getting to me though. No appetite, blurred vision, flat mood, tired easily. I started B12 shots last week so hopefully that helps some. 

I know this is a bit whiney given other possibilities, but I ‘m frustrated.

Hi All,

Personally I wouldn't get to excited with the reduced BM's just yet. These antibiotics are naturally constipating. I was just on the same two for 14 days with the same result but you'll find that as quickly as you slowed down when first taking them you'll more than likely speed up when taken off. Not that your pouchitis won't be cured but your system will speed back up.

Best of luck,



My new GI highly advised I go on Cipro/Flagyl "rotation" after using only Flagyl for a few years (daily) for chronic pouchitis. It's efficacy was starting to  wane anyhow, so I took his advice. Pouchitis always returns when stopping antibiotic. I switch off every 90 days.Cipro makes me feel a little better and it gives me slightly better control. No pouchitis for 1 1/2 years but 6-8 bm is still the norm

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