Should you report diarrhea with omeprazole?

October 12, 2025 •

4 min read

Diarrhea is a recognized side effect of omeprazole, affecting approximately 3.7% of patients in clinical trials. It is important to understand when you should report diarrhea with omeprazole, as symptoms can range from mild and self-limiting to indicators of a serious infection requiring medical attention.

Quick Summary

Diarrhea while taking omeprazole requires evaluation to determine its severity. While often a mild side effect, it can signal a serious infection. This guide explains when to consult a doctor.

Key Points

Diarrhea is a common side effect: Minor, transient diarrhea can occur with omeprazole and is usually not serious.
Report severe diarrhea immediately: Watery or bloody stools, fever, or severe abdominal pain could indicate a serious C. difficile infection and require immediate medical attention.
Omeprazole can alter gut microbiota: The drug's acid-reducing effect can disrupt the normal balance of gut bacteria, which can sometimes lead to diarrhea.
Consult before using anti-diarrheal medication: Do not use OTC anti-diarrheal products for severe symptoms without speaking to a doctor, as they can sometimes worsen infections.
Report persistent symptoms: If mild diarrhea continues for more than two days, talk to your doctor, who may adjust your dose or switch your medication.
Consider FDA MedWatch reporting: You can voluntarily report any adverse drug reactions, including diarrhea, to the FDA to help monitor drug safety.

Omeprazole, marketed under brand names such as Prilosec®, is a proton pump inhibitor (PPI) prescribed to reduce stomach acid and treat conditions like gastroesophageal reflux disease (GERD), ulcers, and erosive esophagitis. While generally well-tolerated, like all medications, it has a range of potential side effects, including gastrointestinal issues like diarrhea. The critical question for patients is how to discern a minor inconvenience from a serious complication.

Understanding the Link Between Omeprazole and Diarrhea

What Causes Omeprazole-Related Diarrhea?

There are two primary reasons omeprazole can cause diarrhea, with one being far more serious than the other. The medication works by decreasing stomach acid, which alters the environment of your digestive tract.

Altered Gut Microbiota: A healthy balance of gut bacteria is essential for proper digestion. Stomach acid plays a role in regulating the population of bacteria in the digestive tract. By suppressing acid production, omeprazole can disrupt this balance, leading to changes in bacterial composition that may cause diarrhea.
Risk of Clostridioides difficile (C. diff) Infection: Long-term or high-dose use of omeprazole has been associated with an increased risk of severe diarrhea caused by an overgrowth of C. difficile bacteria. When stomach acid is reduced, C. difficile bacteria can more easily survive and multiply in the intestines, producing toxins that cause inflammation and watery, potentially bloody diarrhea.

When to Report Diarrhea with Omeprazole to Your Doctor

While mild, occasional loose stools may not be a cause for concern, certain symptoms warrant immediate medical attention. It is crucial to monitor your condition and communicate any significant changes to your healthcare provider.

Seek Immediate Medical Care for Severe Symptoms

You should contact your doctor right away if you experience any of the following, which could indicate a serious infection like C. difficile colitis:

Severe, watery, or persistent diarrhea that does not go away
Fever that develops or persists with diarrhea
Abdominal pain or stomach cramps that are severe or don't improve
Bloody or black, tarry stools
Signs of dehydration, such as decreased urination, dizziness, or lightheadedness

When to Discuss Mild but Persistent Symptoms

If your diarrhea is not severe but continues for more than two days, it is still wise to consult your healthcare provider. Persistent, mild diarrhea could be a sign that your body is not tolerating the medication well or may require dietary adjustments. Never abruptly stop taking a prescribed medication without medical guidance. Your doctor may suggest a different PPI or an alternative acid-reducing medication, such as an H2 blocker.

Comparison of Mild vs. Severe Diarrhea Symptoms


Feature	Mild Omeprazole-Induced Diarrhea	Severe Diarrhea (Potential C. difficile)
Onset	Occurs shortly after starting medication or with dosage change.	Can occur anytime, sometimes months into treatment.
Frequency	Increased bowel movements, but typically manageable.	Frequent, watery stools that are difficult to control.
Duration	Usually resolves on its own within a couple of days.	Persistent, lasting more than two days.
Associated Symptoms	May include mild stomach cramps or gas.	Often accompanied by fever, severe stomach pain, and general feeling of being unwell.
Stool Appearance	Loose or soft stools.	Watery, foul-smelling, and potentially bloody or tar-like stools.
Risk Level	Generally low-risk and resolves with time or dietary changes.	High-risk, life-threatening infection requiring immediate medical care.

Managing Mild Diarrhea and Other Considerations

For mild, short-term diarrhea, certain strategies can provide relief while you await your doctor's advice.

Stay Hydrated: Drink plenty of clear fluids, like water, broth, and electrolyte-replacing sports drinks, to prevent dehydration.
Adjust Your Diet: Follow a bland diet, such as the BRAT diet (bananas, rice, applesauce, toast), and avoid fatty, greasy, or spicy foods. Limit fiber temporarily.
Medication Review: Before using any over-the-counter (OTC) antidiarrheal medication, such as loperamide (Imodium), consult your prescriber or pharmacist. These can worsen C. difficile infections by slowing down the gut, trapping toxins.

Reporting Adverse Events to the FDA

Patients and healthcare professionals can voluntarily report adverse drug events, including diarrhea with omeprazole, to the FDA’s MedWatch program. Reporting helps the FDA monitor the safety of medications after they are on the market and can lead to safety alerts or labeling changes if a pattern emerges. Reporting can be done online or by submitting forms.

Conclusion

While a mild increase in bowel movements can be a normal and manageable side effect when taking omeprazole, it is essential to remain vigilant for signs of a more serious issue. Any severe, persistent, watery diarrhea, especially when accompanied by fever or abdominal pain, should be reported to your doctor immediately. Do not attempt to treat severe diarrhea on your own. By staying informed and communicating promptly with your healthcare team, you can manage your condition safely and effectively. For more details on reporting drug side effects, visit the FDA MedWatch website.

Frequently Asked Questions

Diarrhea from omeprazole is often a mild side effect, but in some cases, it can be a sign of a more serious condition, such as a Clostridioides difficile infection. If your diarrhea is severe, watery, persistent, or accompanied by fever or stomach pain, it is considered serious and requires immediate medical attention.

Symptoms of C. difficile-associated diarrhea often include severe and watery diarrhea, a fever that does not go away, and significant stomach pain or cramping. Unlike mild cases, a C. difficile infection will not resolve on its own and requires prompt medical treatment.

You should not take an OTC anti-diarrheal medication, like Imodium (loperamide), for severe or persistent diarrhea without consulting your healthcare provider. For mild cases, it may be acceptable, but your doctor can confirm safety and rule out more serious causes.

If your diarrhea is mild but lasts more than two days, contact your doctor. They may want to evaluate your symptoms and could recommend dietary adjustments, or they may consider reducing your omeprazole dose or switching to a different medication.

Yes, taking omeprazole, particularly at high doses or for extended periods (e.g., over a year), is associated with a higher risk of developing more serious side effects, including C. difficile diarrhea.

Omeprazole works by reducing stomach acid. This changes the bacterial environment in the gut, which can alter the gut microbiota and sometimes lead to mild diarrhea. For severe cases, the reduction in stomach acid allows harmful bacteria like C. difficile to thrive.

You can report adverse events to the FDA's MedWatch program, which allows patients, consumers, and healthcare professionals to voluntarily report side effects. This can be done online using the MedWatch Online Reporting Form.

Yes, omeprazole can cause other gastrointestinal side effects, including nausea, vomiting, gas, and abdominal pain. If you experience any of these symptoms and they are bothersome, you should discuss them with your healthcare provider.