Why Does Omeprazole Cause Stomach Pain? Gastroenterologist explains.

Our content is not intended nor recommended as a substitute for medical advice by your doctor. Use for informational purposes only.

What you need to know:

Omeprazole causes abdominal pain in 5% of cases. Possible causes include untreated h. pylori infection and the overgrowth of intestinal bacteria. However, abdominal pain can be an association, not a result of omeprazole intake. 

Discuss the issue with your doctor. Don’t stop omeprazole without medical advice. 

Possible causes of stomach pain with omeprazole:

  • A side effect of omeprazole. 5% of patients taking omeprazole experience abdominal pain.
  • Untreated h. pylori infection. 
  • Small intestinal bacterial overgrowth (SIBO).
  • PPIs (as omeprazole) are not your fit. 
  • Stomach pain may be just an association (not due to omeprazole treatment).

1. Omeprazole causes abdominal pain as a side effect.

Abdominal pain is a documented side effect of omeprazole. You have a 5% risk of abdominal pain if you take omeprazole.

The exact mechanism is still not fully understood. The side effects of omeprazole don’t appear to be related to a specific age, dose, or duration of treatment (reference).

Your doctor prescribes omeprazole for conditions such as gastritis, GERD (chronic acid reflux), or peptic ulcer disease. 

Often, these conditions cause abdominal pain (upper-middle stomach pain or heartburn).

During omeprazole treatment, it is not true that every abdominal pain is omeprazole-induced.

For the pain to be omeprazole-induced stomach pain, it has to:

  • Start after taking your omeprazole, or
  • Be different in character (colics or cramps instead of gnawing pain), or
  • Be different in site ( gastritis or peptic ulcer pain is often in the upper-middle part). A change in the location of pain after omeprazole intake may indicate omeprazole-induced stomach pain.
  • Change its intensity after omeprazole (worsening of the same pain after taking omeprazole).

Your pain has to match one of the above criteria before assuming it is due to omeprazole.

2. Untreated h. pylori infection.

H. pylori is a well-known stomach bug (bacteria). It infects your stomach lining. 

It is a frequent risk factor for gastritis, peptic ulcer disease. Some studies also linked h. pylori to GERD (chronic acid reflux).

Omeprazole may cause worsening stomach pain if you take it before treatment of h. pylori. 

Some studies found that inhibiting stomach acid will allow h. pylori to flare up (reference).

The flare-up of the h. pylori infection will worsen gastritis in the long term and causes more stomach pain.

However, this assumption is still controversial. Other studies found that PPIs (such as omeprazole) may result in more acid suppression in h. pylori-infected patients (reference).

Discuss the issue with your doctor if you haven’t been tested for h. pylori.

Treatment of h. Pylori may stop omeprazole from causing abdominal pain. 

3. Small Intestinal Bacterial Overgrowth (SIBO).

Your stomach acid is not pure evil. It is here for a reason.

The main function of your stomach acid is to break down food (especially protein) to prepare it for absorption.

It has another vital function. It kills bacteria and harmful pathogens. Also, your stomach acid prevents the overgrowth of intestinal microorganisms. 

By keeping them under control, stomach acid protects you from the harmful effects of the overgrowth of your intestinal bacteria (reference).

PPIs (as omeprazole) can cause a condition called SIBO (reference). The risk of SIBO increases with the long-term use of omeprazole. 

SIBO can be the reason why omeprazole leads to abdominal pain.

This relation between PPI and SIBO is not fully understood nor confirmed. Discuss the issue with your doctor. Don’t stop omeprazole without permission from your doctor. 

Symptoms of SIBO:

  • Stomach pain or cramps (after taking omeprazole).
  • Nausea, loss of appetite.
  • Diarrhea.
  • Bloating.
  • A feeling of fullness after eating (indigestion).
  • Weight loss.

Learn More about SIBO.

4. PPIs (as omeprazole) are not your fit.

PPIs (as omeprazole) are one of the most widely prescribed and consumed medications. It is also available as an OTC in the USA and many other countries.

The presence or persistence of stomach pain while taking omeprazole doesn’t mean the cause is always omeprazole.

It may be a sign that omeprazole is not effective for your condition. Also, it may indicate other diseases or conditions that resemble gastritis and GERD.

Omeprazole failure to control your abdominal pain may indicate alternative diagnosis such as:

  • Functional dyspepsia.
  • Weakly acidic and biliary reflux.
  • H. Pylori infection.
  • Psychological conditions (anxiety, depression, and others) may present with stomach pain not responding to omeprazole.
  • Functional abdominal pain.


Also, Non-compliance, incorrect dosing, and improper timing of omeprazole lead to its failure. Ineffective omeprazole leads to the persistence of abdominal pain. 

Associated abdominal pain with omeprazole is not always a causal relationship. Work with your doctor to assess the pain type and cause.

Don’t stop omeprazole without consulting your doctor. This may lead to more harmful effects than abdominal pain.