For decades, doctors and public-health officials have given those who have been prescribed antibiotics the same advice: Finish the whole bottle—even if you’re feeling better. But an analysis published yesterday in the British Medical Journal challenges that conventional wisdom.

While you should never stop taking these drugs without your doctor’s okay, the study authors say there may be times when you’re better off not finishing the whole course.

In the analysis, researchers in the U.K. found that the practice of treating all patients with a full “course” of antibiotics—typically seven to 14 days' worth—dates back to when antibiotics first became available in the 1940s, and continues based more on habit than science.

“The 'complete the course' message has become embedded in medical practice despite a lack of evidence to support it,” says Tim Peto, M.D., a professor of medicine and an infectious disease researcher at the University of Oxford, and one of the study's authors.

Peto notes that “when shorter courses have been compared to longer ones, the shorter therapy has nearly always proved just as effective.”

In fact, the BMJ analysis found that shorter courses of antibiotics worked just as well as longer ones to cure infections in six of the seven studies where the length of treatment has been studied. (One study found that a full 10-day course of antibiotics worked better to alleviate the symptoms of bacterial ear infections than stopping the drugs after five days.)

The Risks of Too Many Antibiotics

The idea that patients need to take all their antibiotics, even after they’re feeling better, is based in part on outdated notions about what causes antibiotic resistance, says Lauri Hicks, D.O., a medical epidemiologist at the Centers for Disease Control and Prevention and head of the agency’s program Get Smart: Know When Antibiotics Work.

“If we don’t complete the course of therapy, there is concern that the bacteria that are left over may be more likely to develop resistance to the antibiotic,” Hicks says. “That turns out to be much less of a problem than was originally believed.”

According to Hicks, scientists have come to realize that the larger problem is that antibiotics affect not just the bacteria causing the infection but also the trillions of other bacteria that live in and on your body.

“We have more bacteria in our body than human cells,” she says. And the longer people take antibiotics, the more likely some of those bacteria are to become immune, or resistant, to the drugs.

Overuse of these powerful drugs has led to the widespread development of “superbugs," which cause infections that are extremely difficult to treat. “We are now starting to encounter scary bacteria, such as carbapenem-resistant enterobacteriaceae, or CRE, that are resistant to all known antibiotics,” Hicks says.

Plus the longer you take antibiotics, the more likely you are to wipe out the “good” bacteria in your intestines, Hicks says. That leaves you vulnerable to infection from the bacterium clostridium difficile, or C. diff, which can cause dangerous inflammation, abdominal cramping, and severe diarrhea, and can even be deadly.

Talk to Your Doctor About Antibiotics

About one-third of antibiotics prescribed in doctors’ offices are unnecessary, according to a new report from the CDC. Doctors commonly prescribe these drugs for upper-respiratory illnesses such bronchitis, colds, and the flu, which are caused by viruses—and antibiotics don’t even work against viruses.

“Whenever your doctor recommends an antibiotic, it’s a good idea to ask what it’s for and whether there are other ways you might treat symptoms,” Hicks says. If an antibiotic is warranted, she advises asking what the possible side effects are, and what steps you should take if you start to feel better—or conversely, don’t improve. 

Some serious infections—such as those that affect the heart valves, bones, and bloodstream—require longer treatment with antibiotics to cure the infection, Hicks says. In those cases, it's usually important to finish all the medication prescribed for you.

However, Hicks says that you might be able to shorten the time you take an antibiotic for a less serious illness such as pneumonia, a sinus infection, or urinary tract infection. If you have been fever-free for 24 to 48 hours and are feeling significantly better, “it’s reasonable to call your doctor and ask if you can stop your antibiotic,” she says.

Peto says that patients and doctors should be reassured that “stopping short of a full course of antibiotics won’t worsen the problem of antibiotic resistance.”

If you wind up with leftover antibiotics, don’t hang on to them. Discard unused antibiotics by returning them to the pharmacy or a community take-back program. Or mix the medication with an unpalatable substance such as coffee grounds or kitty litter, seal it in a bag, and throw it out with the household trash. Read more about safe ways to dispose of antibiotics and other unwanted medicines.

Editor's Note: This article and related materials are made possible by a grant from the state Attorney General Consumer and Prescriber Education Grant Program, which is funded by the multistate settlement of consumer-fraud claims regarding the marketing of the prescription drug Neurontin (gabapentin).