How Does Rifaximin Affect Stool and Bowel Habits?

October 17, 2025 •

4 min read

Less than 0.4% of the antibiotic rifaximin is absorbed systemically, allowing it to act almost exclusively within the gastrointestinal tract to target intestinal bacteria. This highly localized action is precisely why it has such a direct and significant impact on stool characteristics and bowel habits during and after treatment.

Quick Summary

Rifaximin modifies stool characteristics by targeting gut bacteria to treat conditions like IBS-D and traveler's diarrhea. Patients typically see normalized bowel movements, but some may experience temporary side effects like constipation, and in rare cases, C. difficile-associated diarrhea can occur.

Key Points

Localized Action: Rifaximin primarily affects the gut by inhibiting bacterial RNA synthesis and is minimally absorbed systemically, allowing it to target GI issues directly.
Treating Diarrhea: It is intended to reduce diarrhea and improve stool consistency for conditions like IBS-D and traveler's diarrhea by rebalancing gut bacteria.
Potential for Temporary Constipation: A side effect of rifaximin can be a temporary change in bowel habits, including constipation, which typically resolves after treatment.
CDAD Risk: A rare but serious risk is Clostridioides difficile-associated diarrhea, which can manifest as severe watery or bloody diarrhea during or up to two months after treatment.
Indirect Effects on HE: For hepatic encephalopathy, rifaximin alters stool by reducing ammonia-producing bacteria, which indirectly affects gut balance and metabolic pathways.
Microbiome Reorganization: Instead of radically altering the microbiome, rifaximin encourages a reorganization toward a more diverse bacterial population, which helps normalize gut function.
Monitoring is Key: Patients should track bowel habits using a scale like the Bristol Stool Form Scale and report any worsening or severe symptoms to their doctor.

The Localized Mechanism of Rifaximin's Action

Rifaximin stands apart from many other antibiotics due to its poor systemic absorption. While most antibiotics are absorbed into the bloodstream to fight infections throughout the body, rifaximin passes through the GI tract largely intact. This makes it a powerful and targeted treatment for conditions rooted in the gut, with minimal impact on the body's overall microbial balance. By binding to the RNA polymerase of bacteria, it prevents them from synthesizing proteins necessary for their survival and replication.

How Rifaximin Rebalances the Gut Microbiome

The antibiotic effect of rifaximin helps to reduce the overgrowth of specific bacteria that cause symptoms in conditions like Small Intestinal Bacterial Overgrowth (SIBO) and Irritable Bowel Syndrome with Diarrhea (IBS-D). In doing so, it helps to restore a healthier bacterial equilibrium. While the exact mechanism is complex and still being studied, it is known that rifaximin can reduce gas-producing bacteria, which in turn can lead to improvements in bloating and abdominal discomfort. It’s important to note that studies suggest rifaximin doesn't induce a radical shift in the overall microbiome composition but rather stimulates a reorganization towards a more diverse and healthier bacterial profile.

Intended Stool Changes from Rifaximin Treatment

The primary goal of rifaximin therapy is to resolve the underlying issues causing specific stool abnormalities. The expected outcome depends heavily on the condition being treated.

For Irritable Bowel Syndrome with Diarrhea (IBS-D)

In patients with IBS-D, rifaximin aims to reduce abdominal pain and normalize bowel function. Clinical studies have shown that treatment can lead to significantly improved stool consistency and a reduction in fecal urgency. The goal is to move the patient's stool consistency from the loose, watery end of the Bristol Stool Form Scale toward a more normal, formed consistency.

For Traveler's Diarrhea (TD)

When treating TD caused by noninvasive strains of E. coli, rifaximin is highly effective at resolving symptoms. Patients can expect to see a shorter duration of diarrhea and a more rapid return to a normal stool form. The median time to last unformed stool is significantly shorter for those treated with rifaximin compared to placebo.

For Hepatic Encephalopathy (HE)

In cases of liver disease leading to HE, rifaximin is used to reduce the amount of ammonia-producing bacteria in the gut. By reducing these bacteria, the level of harmful neurotoxins in the blood decreases, improving neurological function. While not directly aimed at altering stool, this modulation of the gut flora can indirectly affect stool consistency and the overall balance of the digestive system.

Potential Side Effects Affecting Stool

While generally well-tolerated, rifaximin can cause unintended changes in bowel habits as a side effect. Most of these are temporary and subside after the treatment course is completed.

Common Gastrointestinal Side Effects

Constipation: Some individuals may experience constipation while taking rifaximin. This is a potential side effect that is typically temporary.
Bloating and Gas: While rifaximin is often prescribed to reduce bloating, some people may experience it temporarily as their gut bacteria rebalance.
Nausea and Abdominal Pain: General stomach discomfort, nausea, and abdominal pain are common side effects reported by some users.

Serious but Rare Side Effects: Clostridioides difficile-Associated Diarrhea (CDAD)

As with almost any antibiotic, there is a risk of developing Clostridioides difficile-associated diarrhea (CDAD). CDAD is a severe form of diarrhea caused by an overgrowth of C. difficile bacteria. While rare, it is a serious condition that requires immediate medical attention. The symptoms of CDAD include severe, watery or bloody diarrhea, abdominal cramps, and fever. It is crucial to be aware that CDAD can occur during or up to two months after completing rifaximin treatment.

Comparison of Rifaximin's Intended vs. Unintended Stool Effects


Feature	Intended Effect (Therapeutic)	Unintended Effect (Side Effect)
Stool Consistency	Improves consistency in IBS-D and TD patients, reducing diarrhea and urgency.	May temporarily cause constipation or, less commonly, loose stools.
Bowel Frequency	Normalizes bowel movement frequency for those with diarrhea.	Can cause temporary increase or decrease in frequency.
Associated Symptoms	Reduces bloating and abdominal pain associated with conditions like IBS-D.	May cause temporary gas, bloating, nausea, or stomach discomfort.
Timing	Symptom improvement is typically seen within days for acute conditions like TD. For chronic issues like IBS-D, it may take a full course.	Most common side effects occur during the course and resolve afterward. CDAD is a delayed risk.

How to Monitor Your Stool and Symptoms

To help you and your doctor evaluate the effectiveness and manage potential side effects of rifaximin, here are some tips:

Track your symptoms: Keep a diary of your bowel habits, noting the frequency, consistency (using the Bristol Stool Form Scale), and any associated symptoms like pain or bloating before and during treatment.
Stay hydrated: If you experience any temporary diarrhea, drinking plenty of fluids is essential to prevent dehydration.
Be aware of serious signs: If you notice signs of CDAD, such as severe watery or bloody diarrhea, fever, or worsening abdominal pain, contact your doctor immediately.
Follow instructions: Take the medication exactly as prescribed. Stopping too early or skipping doses can not only prevent the treatment from working but also increase the risk of antibiotic resistance.

Conclusion: The Overall Impact

In conclusion, rifaximin significantly and intentionally affects stool and bowel habits by modulating the gut's bacterial environment to treat specific gastrointestinal conditions. For many patients with IBS-D or traveler's diarrhea, this leads to a desired normalization of stool consistency and bowel frequency. However, like any medication, it is not without potential side effects, including temporary changes like constipation or, in rare cases, a serious infection like CDAD. Careful monitoring and adherence to your doctor's instructions are essential to ensure a positive outcome while taking rifaximin. For additional reading on the mechanism of action, you can refer to research published by the National Institutes of Health.

Frequently Asked Questions

For those with Irritable Bowel Syndrome with Diarrhea (IBS-D), the intended effect of rifaximin is to reduce the frequency and looseness of stools. By targeting gut bacteria, it can help normalize bowel movements and improve stool consistency.

Yes, although it is often used to treat diarrhea, a temporary change in bowel habits, including constipation, is a possible side effect for some patients. These effects usually subside after completing the course of medication.

Severe watery or bloody diarrhea is a potential sign of Clostridioides difficile-associated diarrhea (CDAD), a serious infection. You should contact your doctor immediately if you experience these symptoms, even if it is weeks or months after you finish the medication.

Most common gastrointestinal side effects like temporary constipation or gas will typically resolve within a few days or weeks after the last dose. A serious side effect like CDAD requires specific treatment and can occur months later.

No, studies suggest that rifaximin does not induce radical or permanent changes in the gut microbiome. It stimulates a temporary reorganization of the bacterial population, often promoting greater diversity and suppressing harmful bacteria.

Yes, some bloating, gas, and abdominal discomfort can be experienced as a side effect during the rebalancing of the gut flora. However, it is also prescribed to reduce these symptoms in conditions like SIBO and IBS-D.

While black, tarry stools can be listed as a side effect, it can also be a sign of internal bleeding. It is a less common side effect than other changes. Any instance of black or tarry stools should be reported to your doctor immediately.