What are the adverse effects of chronic Proton Pump Inhibitor (PPI) therapy?

Medical Advisory BoardAll articles are reviewed for accuracy by our Medical Advisory Board
Educational purpose only • Exercise caution as content is pending human review
Article Review Status
Submitted
Under Review
Approved

Last updated: June 29, 2025View editorial policy

Personalize

Help us tailor your experience

Which best describes you? Your choice helps us use language that's most understandable for you.

From the Guidelines

Chronic use of Proton Pump Inhibitors (PPIs) is associated with several adverse effects, including increased risk of vitamin and mineral deficiencies, particularly vitamin B12, magnesium, calcium, and iron, as well as potential links to osteoporosis, fractures, and other conditions, as reported in a 2021 study 1. The adverse effects of chronic PPI therapy can be categorized into several key areas, including:

  • Nutrient deficiencies: Long-term PPI use has been linked to decreased absorption of essential nutrients like vitamin B12, magnesium, calcium, and iron, which can lead to anemia, neurological symptoms, or osteoporosis with increased fracture risk over time 1.
  • Increased risk of infections: PPIs may increase the risk of Clostridium difficile infections and other enteric infections by altering gut microbiota and reducing the stomach's natural acid barrier against pathogens 1.
  • Kidney problems: Chronic PPI use has been associated with an increased risk of kidney problems, including acute interstitial nephritis and chronic kidney disease 1.
  • Other potential risks: Some studies suggest associations between PPI use and dementia, cardiovascular events, and community-acquired pneumonia, although these connections remain controversial 1. It is essential to weigh these potential risks against the benefits of PPI therapy and to use the lowest effective dose for the shortest duration necessary, with periodic reassessment of the need for continued therapy 1. Key considerations for clinicians and patients include:
  • Monitoring for signs of nutrient deficiencies and addressing them promptly
  • Being aware of the potential increased risk of infections and taking steps to mitigate this risk
  • Regularly reviewing the need for continued PPI therapy and adjusting the treatment plan as necessary
  • Considering alternative treatments or therapies when possible to minimize the risks associated with long-term PPI use.

From the FDA Drug Label

3 Clostridium difficile-Associated Diarrhea Published observational studies suggest that PPI therapy like pantoprazole sodium may be associated with an increased risk of Clostridium difficile associated diarrhea, especially in hospitalized patients. 5. 4 Bone Fracture Several published observational studies suggest that PPI therapy may be associated with an increased risk for osteoporosis-related fractures of the hip, wrist, or spine. 5. 5 Cutaneous and Systemic Lupus Erythematosus Cutaneous lupus erythematosus (CLE) and systemic lupus erythematosus (SLE) have been reported in patients taking PPIs, including pantoprazole sodium. 5.6 Cyanocobalamin (Vitamin B-12) Deficiency Generally, daily treatment with any acid-suppressing medications over a long period of time (e.g., longer than 3 years) may lead to malabsorption of cyanocobalamin (Vitamin B-12) caused by hypo- or achlorhydria. 5. 7 Hypomagnesemia Hypomagnesemia, symptomatic and asymptomatic, has been reported rarely in patients treated with PPIs for at least three months, in most cases after a year of therapy. 5. 8 Tumorigenicity Due to the chronic nature of GERD, there may be a potential for prolonged administration of pantoprazole sodium. In long-term rodent studies, pantoprazole was carcinogenic and caused rare types of gastrointestinal tumors. 5. 9 Fundic Gland Polyps PPI use is associated with an increased risk of fundic gland polyps that increases with long-term use, especially beyond one year.

The adverse effects of chronic Proton Pump Inhibitor (PPI) therapy include:

  • Increased risk of Clostridium difficile-associated diarrhea
  • Increased risk of osteoporosis-related fractures
  • Cutaneous and systemic lupus erythematosus
  • Cyanocobalamin (Vitamin B-12) deficiency
  • Hypomagnesemia
  • Potential for tumorigenicity
  • Increased risk of fundic gland polyps 2 2

From the Research

Adverse Effects of Chronic PPI Therapy

The adverse effects of chronic Proton Pump Inhibitor (PPI) therapy include:

  • Increased risk of pneumonia, with a 27-39% increase in short-term use 3
  • Association with Clostridium difficile infections, with an odds ratio of 2.15 (95% CI: 1.81-2.55; p < 0.00001) 3
  • Impaired magnesium absorption, with the US FDA issuing a warning regarding fractures associated with PPI use 3
  • Thrombocytopenia, iron deficiency, vitamin B12 deficiency, rhabdomyolysis, and acute interstitial nephritis have also been reported with PPI use 3
  • Nutritional deficiencies, including B12 and magnesium deficiencies 4
  • Rebound acid hypersecretion, acute interstitial nephritis, gastric carcinoid tumor, and cardiovascular risk with clopidogrel and PPI coprescription 4
  • Bone fractures, particularly in susceptible populations 4, 5
  • Enteric infections, including Clostridium difficile and pneumonia 5
  • Acute and chronic kidney disease, gastrointestinal infections, and deficiencies in vitamin B12 and magnesium 5
  • Increased risk of coronavirus disease 2019 and respiratory infections 5

Specific Adverse Effects

Some specific adverse effects of chronic PPI therapy include:

  • Bone fracture: consistently reported in studies, albeit mostly in low-quality data 5
  • Acute and chronic kidney disease: associated with PPI use, although the evidence is mostly based on observational studies 5
  • Gastrointestinal infections: increased risk with PPI use, particularly in studies involving low-quality data 5, 6
  • Magnesium deficiency: consistently reported in studies, although the evidence is mostly based on observational studies 5
  • Vitamin B12 deficiency: associated with PPI use, although the evidence is mostly based on observational studies 5

Clinical Relevance

The clinical relevance of these adverse effects is still being debated, with some studies suggesting a high probability of causality for certain effects, such as increased risk of gastrointestinal infections and rebound acid hypersecretion 6. However, other studies have failed to demonstrate supportive clinical relevance for certain effects, such as acute interstitial nephritis, nutritional deficiencies, and gastric carcinoid 4.

References

Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

Research

Perils and pitfalls of long-term effects of proton pump inhibitors.

Expert review of clinical pharmacology, 2013

Research

Proton pump inhibitors: potential adverse effects.

Current opinion in gastroenterology, 2012

Research

Proton pump inhibitors: Understanding the associated risks and benefits of long-term use.

American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists, 2023

Research

Side Effects of Long-Term Proton Pump Inhibitor Use: A Review.

Basic & clinical pharmacology & toxicology, 2018

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

Have a follow-up question?

Our Medical A.I. is used by practicing medical doctors at top research institutions around the world. Ask any follow up question and get world-class guideline-backed answers instantly.