What are the effects of long-term omeprazole (Proton Pump Inhibitor) use?

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Last updated: June 11, 2025View editorial policy

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From the Guidelines

Long-term omeprazole use can lead to several concerning side effects, and its use should be carefully considered and monitored, particularly in patients with a history of severe erosive esophagitis or GERD-related complications, as discontinuation may lead to recurrence of symptoms or complications 1.

Effects of Long-term Omeprazole Use

The effects of long-term omeprazole use are multifaceted and can impact various aspects of a patient's health. Some of the key concerns include:

  • Nutrient deficiencies: Prolonged use of omeprazole can lead to deficiencies in vitamin B12, magnesium, calcium, and iron, as stomach acid is necessary for proper nutrient absorption 1.
  • Kidney disease: Chronic omeprazole use is associated with an increased risk of kidney disease, including acute interstitial nephritis and chronic kidney disease 1.
  • Infections: Reduced stomach acid can allow more bacteria to survive, increasing susceptibility to certain infections like Clostridium difficile and pneumonia 1.
  • Rebound acid hypersecretion: Long-term users may experience rebound acid hypersecretion when stopping the medication, making discontinuation difficult 1.

Recommendations for Long-term Omeprazole Use

For patients requiring extended acid suppression therapy, the following recommendations can be made:

  • Use the lowest effective dose of omeprazole to minimize the risk of side effects 1.
  • Periodically attempt to discontinue or reduce the dosage of omeprazole under medical supervision to assess the need for ongoing therapy 1.
  • Regularly monitor nutrient levels and kidney function in long-term users, and consider supplementation to prevent deficiencies 1.
  • Carefully weigh the benefits and harms of discontinuing omeprazole in patients with a history of severe erosive esophagitis or GERD-related complications, and quickly re-initiate therapy if symptoms or signs of complicated GERD emerge 1.

From the FDA Drug Label

You should take omeprazole delayed-release capsules exactly as prescribed, at the lowest dose possible and for the shortest time needed. Omeprazole delayed-release capsules can cause serious side effects, including: • A type of kidney problem (tubulointerstitial nephritis). • Diarrhea. • Bone fractures. • Certain types of lupus erythematosus. People who take multiple daily doses of PPI medicines for a long period of time (a year or longer) may have an increased risk of fractures of the hip, wrist, or spine.

The effects of long-term omeprazole use include:

  • Increased risk of bone fractures: People who take multiple daily doses of PPI medicines for a long period of time (a year or longer) may have an increased risk of fractures of the hip, wrist, or spine.
  • Kidney problems: Long-term use of omeprazole may cause a type of kidney problem called tubulointerstitial nephritis.
  • Diarrhea: Omeprazole may increase the risk of getting severe diarrhea, which may be caused by an infection (Clostridium difficile) in the intestines.
  • Lupus erythematosus: Long-term use of omeprazole may cause certain types of lupus erythematosus or have worsening of the lupus that already exists. It is recommended to take omeprazole delayed-release capsules exactly as prescribed, at the lowest dose possible and for the shortest time needed 2.

From the Research

Effects of Long-Term Omeprazole Use

  • Long-term omeprazole therapy is effective for controlling reflux esophagitis, with a low relapse rate of 1 per 9.4 years 3.
  • The treatment is accompanied by a persistent increase in serum gastrin levels, which can lead to micronodular hyperplasia and subatrophic or atrophic gastritis 4.
  • Elevated serum gastrin levels can be reduced by using an alternate-day treatment regimen instead of daily treatment 5.
  • Long-term use of omeprazole may result in adverse effects on hematological and biochemical parameters, including:
    • Reduced red blood cell count and indices 6
    • Elevated cholesterol, triglyceride, and low-density lipoprotein levels 6
    • Increased alkaline phosphatase and aspartate aminotransferase levels 6
    • Elevated creatinine and nitrogen blood urea levels 6
    • Decreased serum ferritin, vitamin D3, and calcium levels 6
  • The American Gastroenterological Association recommends that patients with gastroesophageal reflux disease (GERD) and acid-related complications take a proton pump inhibitor (PPI) for short-term healing, maintenance of healing, and long-term symptom control 7.
  • Patients with uncomplicated GERD who respond to short-term PPIs should attempt to stop or reduce them, and those who cannot reduce PPIs should consider ambulatory esophageal pH/impedance monitoring before committing to lifelong PPIs 7.

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.

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