Madison Avenue has given stomach acid a bad name, but it's really kind of a bum rap. Dip into any physiology textbook, and you'll find that stomach acid serves several constructive purposes. Pepsin, an enzyme that is essential to the preliminary digestion of protein, needs an acidic environment in the stomach to be effective. The strongly acidic hydrochloric acid pumped out by cells in the lining of the stomach also plays a direct role in the early digestion of some foods. And stomach acidity is a built-in barrier to infection: many bacteria and other pathogenic fellow travelers don't make it out of the stomach alive because of the low pH levels they encounter there.

Long-term use

Yet millions of us spend billions of dollars each year on products and medications designed to lessen or get rid of stomach acid. The old standbys, antacids like Maalox and Mylanta, have been supplanted in many cases by drugs that go straight to the source, acting on the cells that produce hydrochloric acid, rather than just neutralizing the acid. Starting in the late 1970s, histamine-2 receptor (H2) blockers like cimetidine (Tagamet), famotidine (Pepcid), and ranitidine (Zantac) came on the market. They were followed by the proton-pump inhibitors, or PPIs, which include esomeprazole (Nexium), lansoprazole (Prevacid), and omeprazole (Prilosec). The PPIs are increasingly the acid reducers of choice because they're far more effective than the H2 blockers. They're also quite a bit more expensive; for example, the over-the-counter version of Prilosec is about twice as expensive as the over-the-counter versions of Pepcid and Zantac.

People take acid-reducing medication for several reasons. PPIs are part of the "triple therapy" used to treat Helicobacter pylori, the bacteria that cause ulcers in the stomach and the upper part of the small intestine (the duodenum). Typically, though, that treatment lasts just one or two weeks. Long-term use of a nonsteroidal anti-inflammatory drug (NSAID) often comes with a long-term acid-reducing prescription. Randomized trials have shown that timely use of PPIs can protect people from getting the ulcers that can develop as a result of NSAID use. Whether PPIs ought to be routinely prescribed with the low doses of aspirin (aspirin is an NSAID) taken to prevent heart attack and strokes is unclear, although some findings suggest that it might be a good idea, and some doctors recommend it for people who are likely to have NSAID-related gut problems.

But the main use of acid reducers is to treat gastroesophageal reflux disease, or GERD, a condition characterized by stomach acid backing up into the esophagus from the stomach. We've all had occasional bouts of reflux and the heartburn pain that it causes. But GERD can be a serious, chronic problem that can lead to terribly painful inflammation of the esophagus (esophagitis), ulceration and bleeding of esophageal tissue, and, in rare instances, esophageal cancer. People with GERD might take an H2 blocker or PPI indefinitely: several studies have shown that in many cases it comes back unless people stay on maintenance therapy.

Like every medication, PPIs occasionally cause side effects, including nausea and headaches. Doctors are aware that PPIs can, in a roundabout way, promote an abundance of gastrin, an important stomach hormone. Too much gastrin could conceivably cause a number of problems, including a rebound effect of extra-heavy stomach acid secretion if people stop taking PPIs. PPIs may interfere with the metabolism of clopidogrel (Plavix). But by and large, PPIs have been viewed as safe medications with few drawbacks.

Yet some patients—and doctors and researchers—have wondered whether suppressing a natural process like stomach acid secretion for long periods might have unintended consequences. A number of studies suggest that there may, in fact, be a few things to worry about. But don't jump the gun: this is an area of research that's still taking shape, and we shouldn't lose sight of the benefits of acid suppression for some people.