Long-Term PPI Risks & Reflux Surgery

In short: Proton pump inhibitors (PPIs) such as omeprazole, pantoprazole and esomeprazole are very effective at reducing stomach acid, and for most people they are safe. Long-term use has been linked in observational studies to problems such as low magnesium, low vitamin B12, bone fractures and some gut infections. However, a large randomized trial found no clear increase in most of these risks. What PPIs cannot do is fix the mechanical problem: the hiatus hernia and the weak valve that let stomach contents come back up. A laparoscopic hiatus hernia repair with a fundoplication rebuilds that valve, and most patients no longer need daily reflux medication afterwards.

“Do I have to take this pill for the rest of my life?” is one of the questions I hear most often in clinic. Many people with reflux have been taking a PPI for years, sometimes decades, and they have read about the possible side effects. Here is a balanced look at what the evidence shows, and why surgery is an option for the right patient.

What PPIs do well

PPIs switch off the acid pumps in the stomach lining. They heal inflamed esophagus (esophagitis), control heartburn for most people, and protect against complications. For some patients, such as those with Barrett’s esophagus, severe esophagitis or a stricture, long-term PPI use is clearly recommended.¹ If your doctor has prescribed one for these reasons, it is doing an important job.

The possible risks of long-term PPI use

Over the past two decades, observational studies have linked long-term PPI use with a range of problems.¹ Some are well established; others are uncertain.

Recognised effects

Worth monitoring

Low magnesium
Low vitamin B12
Gut infections, including C. difficile
Rebound acid when the pill is stopped suddenly

Associations

Less certain

Bone fractures
Kidney disease
Pneumonia
Dementia (later studies have not confirmed this)

Everyday side effects

Usually mild

Headache
Diarrhea or constipation
Bloating or abdominal discomfort

It is important to keep these risks in perspective. An association in an observational study does not prove the pill caused the problem, because people who need long-term PPIs often have other health issues. The best evidence comes from the COMPASS trial, which randomized more than 17,000 people to pantoprazole or placebo for about three years. It found no significant increase in pneumonia, fractures, kidney disease, dementia or death. The one difference was a small increase in gut infections (1.4% vs 1.0%).²

The American Gastroenterological Association’s advice is sensible: take a PPI when there is a clear reason, at the lowest dose that works, and try to reduce or stop it when it is no longer needed.^1,3

Why stopping a PPI can be hard

Many people try to stop and find their symptoms come straight back, sometimes worse than before. Part of this is rebound acid: after weeks on a PPI, the stomach temporarily produces extra acid when the drug is stopped. In a trial of healthy volunteers with no reflux, 44% developed heartburn or indigestion after stopping an eight-week course, compared with 15% on placebo.⁴ This is why PPIs should be tapered under your doctor’s guidance rather than stopped abruptly.

The bigger reason, for people with a hiatus hernia, is that the underlying problem is still there.

What a PPI can’t fix

A PPI makes the stomach contents less acidic. It does not stop them coming up. With a hiatus hernia, the valve at the bottom of the esophagus is displaced and weakened, so food, fluid and bile can still reflux. That is why many patients on PPIs still have regurgitation, a sour taste at night, coughing or hoarseness, or the bloating and difficulty swallowing that come from a larger hernia. You can read more about these symptoms in When does a hiatus hernia actually need surgery?

How surgery can get you off PPIs

A laparoscopic (keyhole) hiatus hernia repair with fundoplication treats the mechanical problem. I bring the stomach back below the diaphragm, close the opening, and wrap the top of the stomach around the lower esophagus to rebuild a one-way valve. The details are in Keyhole hiatal hernia surgery and fundoplication.

~82%of patients needed no long-term reflux medication or redo surgery over a median of 5.6 years⁵

26% vs 82%on PPIs at 5 years: patients who had surgery vs those who stayed on medical treatment⁶

85%still in remission at 5 years after surgery, similar to optimized medication⁷

In a Swedish national study of 2,655 patients, 82% did not need long-term reflux medication or further surgery over a median of 5.6 years.⁵
In the UK REFLUX trial, only 26% of patients who had surgery were taking a PPI five years later, compared with 82% of those who stayed on medication. The surgical group also had better reflux symptom scores.⁶
In the European LOTUS trial, surgery and well-optimized esomeprazole both controlled reflux in most patients at five years (85% and 92%). Surgery achieved this without daily medication.⁷

Surgery is not risk-free. Early swallowing tightness and bloating are common and usually settle, and hernias can come back, especially very large ones (see Why do hiatus hernias come back?). The possible complications are listed on the risks page.

Who is a good candidate?

Reflux proven on testing (endoscopy and pH monitoring), not just heartburn that might have another cause.
A hiatus hernia, especially with regurgitation or obstructive symptoms that a PPI doesn’t control.
Younger patients facing decades of daily medication, or anyone who would rather not take a PPI long term.
Symptoms that respond to a PPI usually predict a good result from surgery.

For patients with a BMI of 35 or more, I discuss combining the repair with weight-loss surgery, because weight is one of the strongest drivers of reflux and of recurrence.

The takeaway: PPIs are effective and, for most people, safe, but they treat the acid, not the hernia. If you are facing a lifetime of daily medication, still have regurgitation despite a PPI, or have a hiatus hernia causing symptoms, keyhole repair with fundoplication is a well-studied way to treat the cause, and most patients come off daily reflux medication. Please don’t stop a PPI without talking to your doctor.

Wondering where you stand? Take the reflux self-assessment, read about hiatus hernia surgery, or see my approach in Dr. Irshad’s Take.

Common questions

Is it safe to take a PPI long term?

For most people, yes, when there is a good reason to take it. Observational studies have linked long-term PPI use with problems such as low magnesium, low vitamin B12, fractures and gut infections, but a large randomized trial of more than 17,000 people found no significant increase in most of these risks apart from a small rise in gut infections. Use the lowest dose that works and review the need with your doctor.

Does pantoprazole or omeprazole fix a hiatus hernia?

No. PPIs reduce stomach acid and can control heartburn, but they do not close the hernia or stop stomach contents from coming back up. Regurgitation and symptoms caused by a large hernia often continue despite a PPI.

Why do my reflux symptoms get worse when I stop my PPI?

Two reasons. Stopping suddenly can cause temporary rebound acid production, and if you have a hiatus hernia, the underlying problem is still there. PPIs should be tapered under your doctor’s guidance rather than stopped abruptly.

Will I be able to stop my PPI after hiatus hernia surgery?

Most patients can. In a national Swedish study, about 82% of patients did not need long-term reflux medication over a median of 5.6 years after laparoscopic antireflux surgery. Results depend on careful patient selection and on the repair technique.

Is hiatus hernia surgery covered by OHIP?

Yes. When it is medically necessary, the operation, anaesthetic and hospital stay are covered by OHIP for Ontario residents.

Dr. Kashif Irshad, MD, MSc, FRCSCThoracic & benign esophageal surgeon. This article is general information, medically reviewed October 2026. About Dr. Irshad →

References

Freedberg DE, Kim LS, Yang YX. The risks and benefits of long-term use of proton pump inhibitors: expert review and best practice advice from the American Gastroenterological Association. Gastroenterology. 2017;152:706–715.
Moayyedi P, Eikelboom JW, Bosch J, et al. Safety of proton pump inhibitors based on a large, multi-year, randomized trial of patients receiving rivaroxaban or aspirin. Gastroenterology. 2019;157:682–691.
Targownik LE, Fisher DA, Saini SD. AGA clinical practice update on de-prescribing of proton pump inhibitors: expert review. Gastroenterology. 2022;162:1334–1342.
Reimer C, Søndergaard B, Hilsted L, Bytzer P. Proton-pump inhibitor therapy induces acid-related symptoms in healthy volunteers after withdrawal of therapy. Gastroenterology. 2009;137:80–87.
Maret-Ouda J, Wahlin K, El-Serag HB, Lagergren J. Association between laparoscopic antireflux surgery and recurrence of gastroesophageal reflux. JAMA. 2017;318:939–946.
Grant AM, Boachie C, Cotton SC, et al. Clinical and economic evaluation of laparoscopic surgery compared with medical management for gastro-oesophageal reflux disease: 5-year follow-up of multicentre randomised trial (the REFLUX trial). Health Technol Assess. 2013;17(22):1–167.
Galmiche JP, Hatlebakk J, Attwood S, et al. Laparoscopic antireflux surgery vs esomeprazole treatment for chronic GERD: the LOTUS randomized clinical trial. JAMA. 2011;305:1969–1977.

This article is general information and is not a substitute for individual medical advice. Please don’t change or stop any medication without talking to your physician.

Long-term PPIs: the risks, and how reflux surgery can get you off them