Can metronidazole cause diarrhea? Understanding this Common Side Effect

October 9, 2025 •

3 min read

Clinical trial data indicate that diarrhea is a known side effect that can affect between 1% and 10% of patients taking metronidazole. This phenomenon is a common concern with many antibiotic treatments, including metronidazole, and is primarily caused by a disruption of the body's natural gut flora.

Quick Summary

Yes, metronidazole can cause diarrhea, a common antibiotic side effect stemming from an imbalance in intestinal bacteria. Symptoms can usually be managed at home, but severe or persistent cases warrant medical consultation to rule out a more serious infection.

Key Points

Prevalence: Diarrhea is a common side effect of metronidazole, affecting 1-10% of patients during or after treatment.
Underlying Cause: The antibiotic disrupts the balance of the gut microbiome, which can allow opportunistic or harmful bacteria like C. difficile to overgrow.
Managing Mild Symptoms: For mild cases, focus on staying hydrated with water and electrolyte solutions, and eat a bland diet (like the BRAT diet) to soothe the digestive system.
Probiotic Use: Probiotics may help restore gut flora balance and can be considered, but should be taken hours apart from the antibiotic dose.
Antidiarrheal Caution: Do not use over-the-counter antidiarrheal medications without a doctor's approval, as they can sometimes worsen antibiotic-associated diarrhea caused by C. difficile.
When to Call a Doctor: Seek immediate medical attention if diarrhea is severe, persistent, bloody, or accompanied by fever or severe abdominal pain, as this could indicate a more serious infection.

The Link Between Metronidazole and Diarrhea

Metronidazole, also known by the brand name Flagyl, is an antibiotic used to treat various bacterial and parasitic infections. Diarrhea is among the most frequently reported side effects associated with its use. This is largely due to the drug's impact on the gut microbiome, the community of microorganisms in the digestive tract.

Metronidazole targets and eliminates harmful bacteria causing an infection. However, in the process, it can also reduce the population of beneficial bacteria essential for healthy digestion. This disruption can lead to an overgrowth of other microorganisms, causing an imbalance that results in diarrhea.

Mechanisms Behind Antibiotic-Associated Diarrhea

Antibiotics, including metronidazole, can cause diarrhea through two main mechanisms:

Gut Microbiome Alteration: By decreasing beneficial bacteria, antibiotics create space for opportunistic pathogens to thrive, disrupting normal digestion and leading to loose stools.
Clostridioides difficile (C. diff) Overgrowth: A more serious cause is when the imbalance allows C. diff bacteria to multiply. These bacteria produce toxins that can inflame the colon, resulting in Clostridioides difficile-associated diarrhea (CDAD). While metronidazole can treat C. diff, some strains are resistant, or symptoms might temporarily worsen during treatment.

Symptoms and Timing

Diarrhea from metronidazole can vary in severity and timing. It might be mild and watery or severe and persistent. Onset can occur during treatment or even weeks after it ends. Other potential gastrointestinal side effects include nausea, abdominal pain, and a metallic taste.

Comparison of Antibiotics and Diarrhea Risk

The risk of diarrhea varies among different antibiotics. Factors include the specific drug, its broadness of action, and its effect on the gut microbiome. Metronidazole carries a moderate risk compared to some other antibiotic classes.


Antibiotic Class	Examples	Relative Risk of Diarrhea	Notes
Nitroimidazoles	Metronidazole	Moderate	Diarrhea is a common side effect, affecting 1-10% of users.
Aminopenicillins	Amoxicillin, Ampicillin	High	A higher risk is associated, especially with combinations like amoxicillin-clavulanate.
Cephalosporins	Cephalexin, Cefixime	High	Considered high-risk, particularly broad-spectrum cephalosporins.
Macrolides	Azithromycin, Erythromycin	Moderate	Can cause diarrhea, though generally less commonly than aminopenicillins.
Lincosamides	Clindamycin	Very High	Historically, one of the highest risks for causing C. difficile overgrowth.

Management Strategies for Metronidazole-Induced Diarrhea

For mild diarrhea while taking metronidazole, management involves staying hydrated with clear fluids and maintaining a bland diet. Avoiding irritating foods like spicy, fatty items, dairy, alcohol, and caffeine is also advised. Probiotics may help restore gut flora, but should be taken at a different time than the antibiotic dose. It's crucial to consult a doctor before using over-the-counter antidiarrheals.

Seek medical attention if diarrhea is severe, persistent, bloody, or accompanied by fever, severe abdominal pain, or signs of dehydration.

Conclusion

Metronidazole can cause diarrhea due to its effect on the gut microbiome, a common issue with antibiotics. Mild cases are manageable with hydration and diet, but awareness of more serious signs like a Clostridioides difficile infection is important for safe treatment completion.

Disclaimer: This article is for informational purposes only and is not a substitute for professional medical advice. Always consult a healthcare provider for any health concerns or before making decisions related to your treatment.

An authoritative resource for further reading on antibiotic side effects is the National Institutes of Health (NIH) website.

Frequently Asked Questions

Diarrhea is a relatively common side effect of metronidazole. According to clinical trial data, it can affect anywhere from 1% to 10% of patients.

Metronidazole, like other antibiotics, can disrupt the natural balance of beneficial bacteria in your gut. This allows opportunistic pathogens to proliferate, leading to an upset stomach and diarrhea.

If you experience mild diarrhea, ensure you stay hydrated by drinking plenty of fluids and electrolytes. Eating a bland, low-fiber diet (bananas, rice, applesauce, toast) can also help firm up your stools.

You should not take over-the-counter antidiarrheal medications like loperamide without first consulting your doctor. In some cases, especially if a C. difficile infection is present, these medications can be harmful.

Contact your healthcare provider immediately if your diarrhea is severe, worsens significantly, is accompanied by a high fever, severe abdominal pain, or if you notice blood in your stools.

Some studies suggest that probiotics can be helpful in preventing and treating antibiotic-associated diarrhea by helping to restore gut flora balance. If you choose to take a probiotic, do so a few hours before or after your antibiotic dose.

Taking metronidazole with food can help reduce some gastrointestinal side effects, such as nausea and upset stomach. While it may help, it does not completely eliminate the risk of diarrhea.