Can Omeprazole Cause Diarrhea? Understanding a Common Side Effect

October 11, 2025 •

4 min read

According to data from clinical trials, diarrhea or loose stools are among the reported side effects for individuals taking omeprazole. While often a mild and manageable issue, understanding the link between this common medication and digestive upset is important for patients.

Quick Summary

Diarrhea is a known, though not universal, side effect of omeprazole, a proton pump inhibitor. The medication can alter the gut's bacterial balance by suppressing stomach acid, leading to mild gastrointestinal distress or, in rare cases, a serious C. difficile infection, especially with long-term use.

Key Points

Diarrhea is a known side effect: Omeprazole has been reported to cause diarrhea or loose stools, though the reaction is often mild.
Altered gut microbiota is the cause: By reducing stomach acid, omeprazole can disrupt the natural balance of bacteria in the intestines, leading to digestive issues.
Serious risk of C. difficile infection: Prolonged omeprazole use can increase the risk of a severe bacterial infection known as Clostridioides difficile (C. diff), which causes severe, watery diarrhea.
Risk increases with dosage and duration: The potential for side effects, particularly serious infections, tends to be higher with long-term use and higher doses of omeprazole.
Management involves hydration and medical advice: For mild diarrhea, staying hydrated and eating a bland diet helps. Severe symptoms require immediate medical attention and should not be treated with over-the-counter medications without a doctor's guidance.
Alternative PPIs are available: If diarrhea is persistent, a doctor may suggest switching to another PPI (like pantoprazole) or a different class of medication (like an H2 blocker), as individual tolerance varies.

Omeprazole, commonly known by the brand name Prilosec, is a proton pump inhibitor (PPI) prescribed to treat conditions like gastroesophageal reflux disease (GERD), peptic ulcers, and erosive esophagitis. Its primary function is to reduce the amount of acid produced in the stomach, providing relief from acid-related symptoms. However, this action can sometimes lead to unintended consequences, including changes in bowel movements. While many people tolerate the medication without any issue, it is a well-documented fact that can omeprazole cause diarrhea as a potential side effect.

The Mechanism Behind Omeprazole-Induced Diarrhea

To understand why omeprazole might lead to diarrhea, it is helpful to first grasp how the medication works. By blocking the proton pump enzyme, omeprazole effectively decreases the stomach's acid production. While this is beneficial for treating acid reflux, it also changes the internal environment of the gastrointestinal tract. Stomach acid normally serves as a crucial line of defense, helping to regulate and control the types of bacteria present in the gut.

When gastric acid is suppressed over time, several changes can occur:

Alteration of Gut Microbiota: The balance of good and bad bacteria in the intestines can be disturbed. This shift in microbial composition, known as dysbiosis, can lead to digestive disturbances like loose stools or diarrhea.
Reduced Nutrient Absorption: Stomach acid is involved in breaking down food and absorbing nutrients. The reduction of acid can affect digestive enzyme activity, potentially impacting how the body processes food.

For most individuals, this effect is mild. However, for a small number of patients, particularly those with other risk factors, the situation can become more serious.

The More Serious Threat of Clostridioides difficile

One of the most significant concerns associated with PPI use is an increased risk of developing a Clostridioides difficile (also known as C. diff) infection. This is a severe bacterial infection that can cause serious, watery diarrhea, abdominal pain, and fever.

The reduced stomach acid from omeprazole creates a more hospitable environment for C. diff bacteria to multiply in the intestines. The risk is particularly heightened with long-term PPI use and in patients who are also taking antibiotics.

Risk Factors and Considerations

Certain factors can increase the likelihood of experiencing diarrhea while on omeprazole:

Long-Term Usage: The risk of C. diff infection and other side effects generally increases with the duration of therapy. Over-the-counter omeprazole is typically recommended for no more than 14 days without medical consultation.
Higher Dosages: Some studies suggest that the frequency of diarrhea may be dose-dependent.
Concurrent Antibiotic Therapy: Taking broad-spectrum antibiotics alongside omeprazole significantly increases the risk of a C. diff infection.
Advanced Age: Elderly patients are more susceptible to complications from altered gut flora and C. diff.
Underlying Health Conditions: Individuals with other chronic medical issues or those in a hospital setting may have a higher risk.

How to Manage Diarrhea Caused by Omeprazole

If you experience mild diarrhea while taking omeprazole, there are several steps you can take to manage your symptoms. However, if symptoms are severe, you should contact a healthcare professional immediately.

Management Steps for Mild Diarrhea

Stay Hydrated: Drink plenty of clear fluids like water, broth, and electrolyte-rich drinks to prevent dehydration.
Adjust Your Diet: Follow the BRAT diet (bananas, rice, applesauce, toast) and avoid fatty, fried, or spicy foods.
Consult Before Using OTC Medications: Do not take over-the-counter anti-diarrheal medications without first speaking to your doctor, especially if the diarrhea is severe, as it can be a sign of a more serious infection.
Monitor Symptoms: Pay close attention to the frequency and nature of your bowel movements. If they become more severe or persistent, seek medical advice.

Omeprazole vs. Other Proton Pump Inhibitors

For those who experience problematic diarrhea with omeprazole, a healthcare provider might consider switching to a different PPI. While all PPIs share a similar mechanism and can potentially cause gastrointestinal side effects, individual tolerance can vary. The following table compares omeprazole with some other common PPIs.


Feature	Omeprazole (Prilosec)	Esomeprazole (Nexium)	Pantoprazole (Protonix)
Availability	OTC and Prescription	OTC and Prescription	Prescription Only
Onset of Action	Faster than many PPIs, but can take days for full effect	Can offer slightly faster symptom relief in some studies	Similar to omeprazole
Diarrhea Risk	Well-documented potential side effect	Similar potential for diarrhea side effects	Similar potential for diarrhea side effects
Drug Interactions	Higher number of known drug interactions compared to other PPIs	Fewer drug interactions than omeprazole	Fewer drug interactions than omeprazole

It is important to note that switching PPIs should only be done under the guidance of a healthcare professional. They can help you weigh the risks and benefits of each medication based on your specific health needs.

Conclusion

In conclusion, omeprazole can cause diarrhea as a recognized side effect, primarily due to its impact on stomach acid levels and the subsequent alteration of gut microbiota. While mild cases can often be managed with dietary adjustments and hydration, the risk of a more severe Clostridioides difficile infection exists, especially with long-term use and other contributing factors. Patients experiencing severe, watery, or bloody diarrhea, fever, or persistent symptoms should contact their doctor immediately. For those who find diarrhea to be a consistent problem, discussing alternative medications, like another PPI with a different side effect profile or an H2 blocker, with a healthcare provider is the safest course of action. The FDA has also issued warnings about the risk of C. diff infections with PPI use, underscoring the importance of careful usage.

For more detailed guidance on the potential risks associated with PPIs, review the FDA's safety communication regarding Clostridium difficile-associated diarrhea in patients using stomach acid-reducing drugs.

Frequently Asked Questions

Diarrhea is considered one of the more common side effects of omeprazole, reported by a minority of users in clinical trials. Most cases are mild, but it's important to be aware of the possibility.

Omeprazole reduces stomach acid, which normally helps control intestinal bacteria. This acid reduction can create an environment where the C. difficile bacterium can thrive, potentially leading to a severe infection, especially with long-term or high-dose use.

If you experience mild, loose stools shortly after starting omeprazole, it may be a side effect. However, if you develop severe, watery, or bloody diarrhea, or experience fever and abdominal pain, it could be a sign of a C. difficile infection, and you should seek medical attention.

If the diarrhea is mild, focus on staying hydrated with plenty of fluids. Eating bland foods (like the BRAT diet: bananas, rice, applesauce, toast) can also help manage symptoms. Avoid fatty and fried foods.

You should not take over-the-counter anti-diarrheal medications without first consulting your healthcare provider. It's crucial to rule out a more serious infection like C. difficile before treating the symptoms.

It is possible. While all PPIs share a similar mechanism, individual tolerance varies. A doctor might suggest switching to a different PPI, like pantoprazole, which may have a slightly different side effect profile or fewer drug interactions. Any changes should be medically supervised.

Seek immediate medical help if you experience severe, persistent, or watery diarrhea, especially if it contains blood. Other warning signs include fever, abdominal pain, and symptoms that do not improve after a few days.

The risk of diarrhea and other side effects is generally highest while actively taking the medication. If omeprazole is the cause, the symptoms should subside after stopping the drug, but any changes to your treatment plan should be made in consultation with your doctor.