Omeprazole (Prilosec, Zegerid) is a commonly used medicine for problems associated with stomach acid, such as heartburn, acid reflux and digestive system ulcers. It is available by prescription and over the counter. Omeprazole has been taken by many people worldwide and is usually well tolerated. It can, however, cause a variety of side effects, most commonly affecting the digestive and nervous systems. Most side effects are mild, but discuss any concerns with your doctor.

Digestive System

First approved in the United States in the late 1980s, omeprazole has a long history of use. A hallmark study published in October 1991 in "Digestive Diseases and Sciences" reported that among roughly 3,000 people taking omeprazole, digestive system side effects were most frequent, although uncommon 1. Approximately 4 percent of omeprazole users experienced abdominal pain, stomach upset and/or flatulence.

Omeprazole also appears to increase risk for a severe, persistent type of diarrhea called Clostridium difficile-associated diarrhea, or CDAD. Reduced stomach acid production degrades your ability to combat the bacteria that causes CDAD. This condition can cause life-threatening complications, including ulcers and bowel rupture. Contact your doctor immediately if you experience abdominal pain, persistent diarrhea and/or fever while taking omeprazole.

Nervous System

Headache occurs in about 7 out of every 100 people taking omeprazole, according to the authors of the "Digestive Diseases and Sciences" study report 1. Dizziness occurs in less than 2 percent of omeprazole users, according to the U.S. Food and Drug Administration-approved prescribing information 6.

Respiratory System

A study published in October 2004 in "JAMA" examined the risk for pneumonia among more than 364,000 people according to their use of stomach acid-suppressing drugs, such as omeprazole 5. The researchers found that people currently taking acid suppressants had an increased risk of developing pneumonia, compared to those not taking these medicines. Doctors believe the increased risk is due to growth of bacteria normally killed by stomach acid, which can then infect the lungs. Contact your doctor right away if you develop a cough, shortness of breath and/or fever while taking omeprazole, as these symptoms might indicate pneumonia.

Long-Term Side Effects

Reduced bone strength with an increased risk of fractures is possible with long-term omeprazole use. This risk occurs primarily in people who take multiple doses daily for a year or longer. Long-term omeprazole use might also cause low levels of magnesium and/or vitamin B12, although these changes are rare. The risk of vitamin B12 deficiency typically occurs only in people who have taken omeprazole daily for 3 years or longer. Low magnesium levels have been reported primarily in people who have been on daily omeprazole for a year or longer, but might occur in a shorter time frame. Rarely, long-term omeprazole therapy can lead to potentially harmful changes in the stomach or kidneys.

Warnings and Precautions

As with any drug, an allergic reaction is possible with omeprazole. People who are allergic to medicines used to treat worm infestations -- including albendazole (Albenza) and mebendazole -- should not take omeprazole because it is likely to cause a serious allergic reaction.

Omeprazole is classified as an FDA pregnancy category C drug, meaning animal studies have shown possible harm to a developing fetus, but there are no conclusive human studies. Omeprazole also crosses into breast milk. Women who are pregnant or nursing should talk with their doctor before taking omeprazole.

If you experience frequent or persistent heartburn or stomach-related symptoms, see your doctor for diagnosis and treatment.