Food often gets the blame for digestive distress. But be careful what else you put in your mouth—many medications, even over-the-counter meds, have digestive side effects. Here are three meds that are common sources of stomach woes when not used wisely.

Antibiotics and the Digestive Aftermath

Antibiotics seek to wipe out unwanted infectious agents, but there's collateral damage. "An antibiotic is like an atomic bomb exploding in the colon," says Patricia Raymond, MD, a fellow of the American College of Gastroenterology. "Healthy microbes die indiscriminately." Suddenly the hardier, harmful bacteria that the good guys would normally keep in check are able to multiply. Watch for bloating and diarrhea after taking an antibiotic—sure signs you've disturbed your gut flora. To avoid that:

Invite antibiotics in carefully—not for the common cold.

"Don't think every sniffle or sneeze begs for an antibiotic," says Dr. Raymond, who notes that antibiotics are powerless against colds and the flu anyway. "If you need an antibiotic, take one that attacks the specific bacterial infection you have. A broad-spectrum drug like Cipro pretty much wipes out all existing life forms in the vicinity."

Protect your digestive system with a probiotic.

Taking a probiotic while you're on an antibiotic (and then for four to six weeks afterward) can help lessen the digestive side effects.

The Best Help When Heartburn Hits

Let's say reflux won't leave you alone. Chances are you'll reach for an acid-suppressing drug. The problem is, acid may not be why you're refluxing; if it happens more than twice a week, it could be gastroesophageal reflux disease. The problem lies with the valve separating your esophagus from your stomach. What's more, neutralizing that acid can harm your gut. Stomach acid is there for a reason: to handle live bacteria in our diet. To get relief:

Ditch the conventional antacids.

Take a version called Gaviscon instead, says Dr. Raymond. "It contains a compound called alginate that doesn't try to neutralize all of the acid," she says. "It floats on top of the acid, creating a foamy barrier that prevents burning sensations."

Move heartburn on its way.

The longer food sits in your stomach, the likelier it will attempt a comeback. Going for a 30-minute walk will help usher food into the intestine.

Pain Relief While Protecting Your Stomach

Nonsteroidal anti-inflammatory drugs (NSAIDs), such as aspirin and ibuprofen, are kryptonite for your gut. Using them for acute pain, like a major headache, is fine once in a while. But popping them like M&M's can lead to stomach ulcers by decreasing prostaglandins that produce the mucus that normally seals your stomach. Acid can then escape and wreak havoc.

Aside from the pain and bleeding they cause, ulcers can deform and scar your stomach. A perforation, for example, is a hole that can extend all the way through your stomach lining to your abdomen—which is not the place you want lunch emptying. Perforations can be quite serious, usually requiring surgical repair. To minimize your risk:

Know stomach-friendly choices.

Switch to Tylenol, since acetaminophen won't damage your stomach lining the way NSAIDs do. Deglycyrrhizinated licorice (DGL), an herbal supplement, has been used to help heal the stomach's mucous membrane, safeguarding it from stomach acid. So chew 350 milligrams of DGL along with that ibuprofen if you're an occasional pill popper, or take it before meals and bedtime if you're a chronic user. Just make sure not to grab licorice or licorice root instead. Both contain glycyrrhizic acid, the blood-pressure-boosting compound that's been removed from DGL.

Avoid taking NSAIDs on an empty stomach.

"Food can buffer their negative effects on the gut, in part by keeping them from being absorbed too quickly," says Dr. Raymond. So enjoy permission to snack.