8 Omeprazole Side Effects You Should Know About
Key takeaways:
Omeprazole (Prilosec) is available as an over-the-counter medication to provide heartburn relief. It’s also available with a prescription to treat conditions like gastroesophageal reflux disease (GERD).
The most common omeprazole side effect is headache. But it can also cause stomach-related side effects, such as nausea, vomiting, or diarrhea.
Taking omeprazole at high dosages, or for longer than a year, raises the risk of more serious side effects. These can include bone breaks and pneumonia (a lung infection).
Access savings on related medications
Table of contents
If you have heartburn, you might consider taking omeprazole (Prilosec). This medication is available over the counter (OTC) for heartburn. But it’s also available by prescription to treat conditions such as gastroesophageal reflux disease (GERD).
Omeprazole belongs to a group of medications called proton pump inhibitors (PPIs). PPIs help lower acid levels in the stomach to reduce symptoms of heartburn and GERD. Omeprazole is generally well-tolerated. But as with any medication, there are some side effects you should be aware of while taking it.
Omeprazole side effects at a glance
Below is a list of common, as well as rare but serious, omeprazole side effects reported in clinical studies. Keep in mind that other side effects are possible, so don’t hesitate to bring any concerns to a healthcare professional while taking omeprazole.
Get Lantus For Less
With GoodRx, pay no more than $35 for a 30 day supply of Lantus.
GoodRx is NOT insurance. GoodRx Health information and resources are reviewed by our editorial staff with medical and healthcare policy and pricing experience. See our editorial policy for more detail. We also provide access to services offered by GoodRx and our partners when we think these services might be useful to our visitors. We may receive compensation when a user decides to leverage these services, but making them available does not influence the medical content our editorial staff provides.
Common omeprazole side effects include:
Headache
Stomach pain
Nausea and vomiting
Diarrhea
Gas
Constipation
Dizziness
Upper respiratory tract infections
Rare but serious omeprazole side effects include:
Low vitamin B12 levels
Low magnesium levels
Stomach polyps (non-cancerous growths)
Kidney problems
Clostridioides difficile diarrhea
Increased risk of bone fracture
Severe skin reactions
Let’s take a closer look at eight notable omeprazole side effects and how you might manage them.
1. Headache
Headache is the most common omeprazole side effect. Around 7% of people in clinical trials for omeprazole reported having a headache. Typically, this side effect is mild and doesn’t require medical attention.
One study found that the risk of headaches is highest within the first 7 days of starting a PPI. Researchers also noted that women were more likely to experience this side effect.
If you get a headache while taking omeprazole, you may be able to take OTC pain relievers, such as acetaminophen (Tylenol). But medications like ibuprofen (Advil) might make GERD symptoms worse. So it’s best to talk with your healthcare team about which OTC pain reliever may be best for you.
2. Stomach pain
The second-most common omeprazole side effect is stomach pain. It was reported by about 5% of people in clinical trials.
Stomach pain (abdominal pain) includes pain you feel anywhere between your chest and groin. It can be hard to tell if stomach pain is due to omeparzole, the condition you’re taking omeprazole for, or something else altogether. And stomach pain can sometimes be a sign of a more serious health problem. So it's important to seek medical care if you have stomach pain that won’t go away while taking omeprazole.
3. Nausea and vomiting
It’s also possible to experience nausea or vomiting when taking omeprazole. Sometimes, taking medication with food can help prevent these side effects. But omeprazole works best when taken on an empty stomach, about 30 to 60 minutes before a meal. So taking your dose with food isn’t the best way to manage this omeprazole side effect.
Other things that might help include eating multiple small meals throughout the day. You can also try eating bland foods for a few days, or staying upright for a while after eating. Medications that relieve nausea might be an option for some people. But omeprazole interacts with several medications. So check with your prescriber or pharmacist before taking any other medications with it.
Good to know: Nausea could also be a symptom of kidney problems. Kidney damage from omeprazole is rare, but it’s possible. If you have nausea along with extreme tiredness, changes in urination, or swelling, seek medical care right away.
4. Gas
Omeprazole can also make you have more gas than usual. This can be uncomfortable, causing bloating, cramps, or flatulence. Omeprazole can also cause constipation, which can cause similar symptoms, though this isn’t as common.
Lifestyle changes, such as drinking more water and exercising, can help relieve constipation. This might also lower the amount of gas you have. You can also try an OTC gas relief medication, such as simethicone (Gas-X).
If you have painful gas, or gas that doesn’t go away, seek medical care. Severe gas isn’t a typical omeprazole side effect.
Stop the burning. Real people share what it’s like to take omeprazole for heartburn.
How long does it take for omeprazole to work? Pharmacist-backed answers to this and more common questions about omeprazole.
Omeprazole tips: GoodRx pharmacists cover a few things you should know about omeprazole.
5. Diarrhea
Some people taking omeprazole might experience diarrhea. You can often manage diarrhea with dietary changes, such as avoiding fatty and fried foods. Be sure to drink plenty of fluids to prevent dehydration.
Some people also find OTC diarrhea medications are helpful. Examples include bismuth subsalicylate (Pepto-Bismol) and loperamide (Imodium A-D). But check with your prescriber or pharmacist first to avoid any possible interactions.
While diarrhea with omeprazole is common, it can also be a symptom of a more serious side effect. Omeprazole can raise your risk of a bacterial infection called Clostridioides difficile (C. diff) diarrhea. C. diff infections are more likely if you take omeprazole long term. This is why it’s recommended to use the lowest possible dose of omeprazole for the shortest time needed. And you shouldn’t take OTC omeprazole for longer than 2 weeks without a healthcare professional’s OK.
C. diff infections can be life-threatening and require medical attention. If you have severe, watery diarrhea, fever, or stomach pain that doesn’t go away, seek medical care right away.
6. Bone fractures
Omeprazole raises the risk of bone fractures (breaks). This may be of extra concern if you have osteoporosis or are at risk of developing it.
In studies, bone fractures linked to omeprazole were most commonly reported in the wrists, hips, and spine. Taking low doses of omeprazole for short periods of time can help lower your risk of this side effect.
If you need to take omeprazole long term, talk to your prescriber about ways to prevent bone fractures. One thing they might suggest is making sure you’re getting enough calcium and vitamin D.
7. Respiratory infections
Omeprazole lowers stomach acid levels, which is good for conditions like GERD. But stomach acid plays an important role in fighting off bad bacteria. Less stomach acid can allow bacteria in your stomach to overgrow and spread to your lungs. This may lead to respiratory infections. There’s also some evidence that long-term PPI use (3 to 6 months) may raise the risk for pneumonia (a lung infection).
Seek medical care if you have a cough, fever, or shortness of breath while taking omeprazole. These can be potential symptoms of a respiratory infection.
8. Low magnesium levels
Another long-term omeprazole side effect is low magnesium levels. In many cases, low magnesium causes no symptoms. But in severe cases, very low magnesium can cause muscle spasms, seizures, or abnormal heart rhythms.
Low magnesium can happen if you’ve taken omeprazole for at least 3 months. But the longer you take omeprazole, the greater your risk may be. If you take other medications that lower magnesium, such as digoxin (Lanoxin), you may be more prone to this omeprazole side effect.
Your prescriber may check your magnesium levels regularly if you’re taking omeprazole long term. Keeping these appointments can help your prescriber catch and correct this omeprazole side effect early if it occurs.
Frequently asked questions
For omeprazole to work at its best, it should be taken on an empty stomach. It’s also a good idea to avoid foods that may worsen your heartburn or GERD symptoms. This includes spicy, fatty, and acidic foods, such as tomatoes, garlic, and citrus fruits. It’s also best to avoid or limit coffee, soda, and alcohol.
It may be safe to take omeprazole while you’re pregnant. It hasn’t been associated with an increased risk of birth defects, miscarriage, or other issues. But it’s best to check with your prenatal care team before taking any medications while pregnant. They can make a recommendation based on your personal history.
It’s best to take omeprazole on an empty stomach about 30 to 60 minutes before breakfast. This helps ensure it can work at its best. Keep in mind that you need to take omeprazole consistently in order for it to work. It isn’t an “as-needed” medication the way that antacids are.
The bottom line
Omeprazole (Prilosec) is usually well-tolerated. But it can cause headaches and stomach-related side effects, such as nausea, gas, or diarrhea. Long-term use can lead to more serious omeprazole side effects, such as respiratory infections or bone fractures.
Taking the lowest effective omeprazole dosage for the shortest amount of time necessary can help you avoid serious side effects. Don’t take omeprazole long-term without a healthcare professional’s OK. And seek medical care for any side effects that are severe or bothersome.
Why trust our experts?
References
Asclemed USA. (2025). Omeprazole capsule, delayed release [package insert].
Herdiana, Y. (2023). Functional food in relation to gastoesophageal reflux disease (GERD). Nutrients.
Liang, J., et al. (2014). Proton pump inhibitor-related headaches: A nationwide population-based case-crossover study in Taiwan. Cephalagia.
MotherToBaby. (2024). Omeprazole | esomeprazole.
Nguyen, P. A., et al. (2020). Meta-analysis of proton pump inhibitors induced risk of community-acquired pneumonia. International Journal for Quality in Health Care.
Pasternak, B., et al. (2010). Use of proton-pump inhibitors in early pregnancy and the risk of birth defects. The New England Journal of Medicine.
Ruszniewski, P., et al. (2008). Nonsteroidal anti-inflammatory drug use as a risk factor for gastro-oesophageal reflux disease: An observational study. Alimentary Pharmacology and Therapeutics.
U.S. Food and Drug Administration. (2017). FDA drug safety communication: Clostridium difficile associated diarrhea can be associated with stomach acid drugs known as proton pump inhibitors (PPIs).
U.S. Food and Drug Administration. (2017). FDA drug safety communication: Low magnesium levels can be associated with long-term use of proton pump inhibitor drugs (PPIs).
U.S. Food and Drug Administration. (2017). FDA drug safety communication: Possible increased risk of fractures of the hip, wrist, and spine with the use of proton pump inhibitors.
Zirk-Sadowski, J., et al. (2018). Proton-pump inhibitors and long-term risk of community-acquired pneumonia in older adults. Journal of the American Geriatrics Society. Asclemed USA. (2025). Omeprazole capsule, delayed release [package insert].
Herdiana, Y. (2023). Functional food in relation to gastoesophageal reflux disease (GERD). Nutrients.
Liang, J., et al. (2014). Proton pump inhibitor-related headaches: A nationwide population-based case-crossover study in Taiwan. Cephalagia.
MotherToBaby. (2024). Omeprazole | esomeprazole.
Nguyen, P. A., et al. (2020). Meta-analysis of proton pump inhibitors induced risk of community-acquired pneumonia. International Journal for Quality in Health Care.
Pasternak, B., et al. (2010). Use of proton-pump inhibitors in early pregnancy and the risk of birth defects. The New England Journal of Medicine.
Ruszniewski, P., et al. (2008). Nonsteroidal anti-inflammatory drug use as a risk factor for gastro-oesophageal reflux disease: An observational study. Alimentary Pharmacology and Therapeutics.
U.S. Food and Drug Administration. (2017). FDA drug safety communication: Clostridium difficile associated diarrhea can be associated with stomach acid drugs known as proton pump inhibitors (PPIs).
U.S. Food and Drug Administration. (2017). FDA drug safety communication: Low magnesium levels can be associated with long-term use of proton pump inhibitor drugs (PPIs).
U.S. Food and Drug Administration. (2017). FDA drug safety communication: Possible increased risk of fractures of the hip, wrist, and spine with the use of proton pump inhibitors.
Zirk-Sadowski, J., et al. (2018). Proton-pump inhibitors and long-term risk of community-acquired pneumonia in older adults. Journal of the American Geriatrics Society.
Was this page helpful?
Related Articles
Browse medications
View AllResearch prescriptions and over-the-counter medications from A to Z, compare drug prices, and start saving.