Key takeaways:
Omeprazole (Prilosec) is a proton pump inhibitor that reduces stomach acid. It’s available both over the counter and with a prescription.
Common omeprazole side effects include headaches and stomach-related side effects, such as nausea, vomiting, or diarrhea.
More serious omeprazole side effects include respiratory infections, low magnesium levels, and an increased risk of bone fractures. These side effects are more likely if you take omeprazole long term.
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If you have heartburn, you might consider taking omeprazole (Prilosec). This medication is a popular over-the-counter (OTC) heartburn medication. 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 reduce stomach acid levels to treat heartburn and GERD symptoms. 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
Common, as well as rare but serious, omeprazole side effects are listed below. Many serious omeprazole side effects are related to long-term use of omeprazole. Taking the lowest effective dose for the shortest time needed can help keep side effects to a minimum.
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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:
Very low vitamin B12 levels
Very low magnesium levels
Stomach polyps (non-cancerous growths)
Kidney problems
Clostridioides difficile (C. diff) diarrhea
Increased risk of bone fractures
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. Typically, this side effect is mild and will resolve on its own.
If you get a headache while taking omeprazole, try applying a cool compress or lying down in a dark room. If needed, talk to your prescriber about taking acetaminophen (Tylenol) for headache pain. But it’s best to avoid nonsteroidal anti-inflammatory drugs (NSAIDs), such as ibuprofen (Advil, Motrin). They can worsen heartburn.
2. Stomach pain
Stomach pain is another common omeprazole side effect. Keep in mind that heartburn and GERD can also cause stomach pain. So this symptom may improve as omeprazole starts working.
But you should report any new or worsening stomach pain that appears while taking omeprazole to your healthcare team. This could be a sign of something more serious that requires medical attention, such as a stomach ulcer.
3. Nausea and vomiting
It’s also possible to experience nausea or vomiting while taking omeprazole.
Omeprazole works best when you take it 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 nausea. Instead, try eating smaller meals or often throughout the day. You can also try eating bland foods for a few days, or staying upright for a while after eating.
If nausea is bothersome, talk to your prescriber for guidance. Medications that relieve nausea might be an option. But omeprazole interacts with several medications. Your prescriber can review your medication list and recommend something that’s safe for you.
Good to know: Nausea can sometimes 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 while taking omeprazole, seek medical care right away.
4. Gas
Omeprazole can make you more gassy 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 regularly, can help relieve gassiness and manage constipation. You can also try an OTC gas relief medication, such as simethicone (Gas-X).
If you have painful gas or gassiness that doesn’t go away, seek medical care. Severe gas isn’t a typical omeprazole side effect.
5. Diarrhea
Some people taking omeprazole might experience diarrhea. You can often manage diarrhea with dietary changes, such as avoiding fatty and fried foods and gradually increasing your fiber intake. Be sure to drink plenty of fluids to prevent dehydration.
Some people also find OTC diarrhea medications 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 C. diff diarrhea. C. diff infections are more likely if you take omeprazole long term. This is why it’s recommended to take 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 while taking omeprazole, seek medical care right away.
6. Bone fractures
Omeprazole raises the risk of bone fractures (breaks) if you take it for a long period of time. This may be of extra concern if you’re living with 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 the lowest effective dose of omeprazole for the shortest amount of time needed can help lower your risk of this side effect.
If you need to take omeprazole long term, talk to your prescriber about ways to help 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. With less stomach acid, bacteria in your stomach may overgrow and spread to your lungs. This can lead to respiratory infections.
There’s also some evidence that taking omeprazole and other PPIs for 3 months or longer may raise the risk of pneumonia (a lung infection).
Seek medical care if you develop 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.
In general, it seems that the longer you take omeprazole and the higher your dosage, the greater your risk of developing low magnesium levels. 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 if it occurs.
Frequently asked questions
You should take omeprazole on an empty stomach in order for it to work at its best. So you should avoid food in general for 30 to 60 minutes after your dose. 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 meals. If you take it once a day, before breakfast is best. 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.
Omeprazole has several drug interactions to be aware of before you start taking it. These include warfarin (Coumadin, Jantoven), citalopram (Lexapro), and some HIV medications. It also interacts with the supplement St. John’s wort. It’s best to review your current medication list with your pharmacist or prescriber before taking omeprazole to make sure it’s safe for you.
You should take omeprazole on an empty stomach in order for it to work at its best. So you should avoid food in general for 30 to 60 minutes after your dose. 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 meals. If you take it once a day, before breakfast is best. 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.
Omeprazole has several drug interactions to be aware of before you start taking it. These include warfarin (Coumadin, Jantoven), citalopram (Lexapro), and some HIV medications. It also interacts with the supplement St. John’s wort. It’s best to review your current medication list with your pharmacist or prescriber before taking omeprazole to make sure it’s safe for you.
The bottom line
Common omeprazole (Prilosec) side effects include 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, low magnesium levels, and an increased risk of bone fractures.
Taking the lowest effective omeprazole dosage for the shortest amount of time needed 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.
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References
Dr. Reddy’s Laboratories Limited. (2026). Omeprazole capsule, delayed release [package insert].
Herdiana, Y. (2023). Functional food in relation to gastoesophageal reflux disease (GERD). Nutrients.
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.
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).
Wang, L., et al. (2017). Proton pump inhibitors and the risk for fracture at specific sites: Data mining of the FDA adverse event reporting system. Scientific Reports.
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.
