If you have gastroesophageal reflux disease (GERD) and take medication to control your symptoms, you're probably wondering what the long-term effects are. In this article Dr. Sergey V. Kantsevoy and his team of gastroenterologists at Johns Hopkins answer the question: What are the risks of taking reflux medication over the long term?

The contents of your stomach are emptied into the small intestine, but sometimes they flow backwards into your esophagus. This phenomenon, known as gastroesophageal reflux, happens to everyone from time to time. It usually produces no symptoms other than occasional heartburn -- a burning sensation behind the breastbone. When gastroesophageal reflux occurs frequently, however, you may begin to experience significant discomfort related to the acid reflux -- then, it is considered gastroesophageal reflux disease (GERD).

GERD is a serious condition because the acid and digestive enzymes from the stomach can damage tissues in the esophagus as well as in adjacent organs such as the mouth, pharynx (throat), larynx (voice box), trachea (windpipe), and lungs.

Medications for GERD like proton pump inhibitors and H2-blockers are generally very safe. But as with any drugs, their beneficial effects are often offset by some negative consequences. The most serious potential complications of GERD medication result from the reduction of stomach acid that actually protects your body from bacteria and viruses that may be present in food. Without sufficient acid levels, stomach bacteria are allowed to grow—and travel up or down the digestive tract.

For example, there’s a small chance that stomach bacteria may enter your trachea and upper airways, resulting in pneumonia. Or you may not have enough acid to fight off a serious intestinal infection from a bacterium like Clostridium difficile (C. difficile), which causes colitis, diarrhea, and cramps. Your body also needs stomach acid to help digest vitamin B12. Without sufficient levels of stomach acid, you could develop low vitamin B12 levels and, subsequently, anemia.

Bottom line advice on GERD medications: All of these potential complications are rare and treatable, so for most people, taking GERD medication does more good than harm -- especially if you have esophagitis or Barrett’s esophagus. If your GERD isn’t severe, talk with your doctor about taking your medication as needed, rather than continuously.