Is the pill sabotaging your gut health?

The birth control pill is amazing in so many ways. It’s a super effective means of preventing unwanted pregnancies and can help with terrible periods, painful endometriosis, and acne. For a lot of women, the pill is a godsend. But for those who are gut health-savvy—eating lots of fiber, making kimchi, and even drinking probiotic cold brew—the pill might be undermining your efforts, say experts.

Some researchers and doctors are now cautioning women that hormonal birth control—particularly the pill—might be taking a toll on their gut health. That nagging bloat or persistent gas you’re feeling? It’s not necessarily a symptom of your period, or even a side effect of birth control. It could be a red flag that the pill is throwing your gut out of whack, and in the process undermining your overall wellness.

“We are now understanding how powerful the role of the microbiome is in our health,” says functional medicine physician Robin Berzin, MD, founder of Parsley Health. “And the things that alter our microbiomes most are chronic medications, like the pill.”

You have hormone receptors everywhere in your digestive tract, echoes Inner Source Health’s Peter Bongiorno, ND, Lac, a naturopath, acupuncturist, and author of Put Anxiety Behind You. The added hormones in your body from the pill can affect those receptors, and sometimes the result is pretty extreme, he says. 

“For women who take birth control for greater than five years, there is a three-fold increased risk of Crohn’s disease,” says Bongiorno, referring to a sweeping study published last year. That’s not to say that it causes Crohn’s disease; rather, that it can majorly up the risk in people with a strong genetic predisposition to the inflammatory bowel disease in the first place.

“The things that alter our microbiomes most are chronic medications, like the pill.”

Of course, for most women the signs that the pill is messing with gut health are more subtle and not as easy to pin down. Irritable bowel syndrome, gas, bloating, and constipation can all be signs of “dysbiosis,” or a microbial imbalance within the digestive tract, says Dr. Berzin. So are acne and eczema. She often finds that a patients goes off the pill and works with her to improve her microbiome through a combo of diet, probiotics, and certain herbal supplements, the skin problems she thought were hormonal in origin clear right up.

The big question, of course, is where does this leave women who are in need of a good, reliable contraceptive option?

Both Dr. Berzin and Bongiorno said the IUD is generally a better bet than the pill when it comes to gut health, partly because it’s not ingested directly, and partly because there are non-hormonal options. For other women, condoms or natural family planning methods might be a fit. 

The really critical thing is to play detective if something feels off, and to talk to your doctor about it. No one should have to accept general gut malaise as the cost of being a sexually active adult—but the good news, according to Bongiorno, is that mainstream medicine is getting hip to the potential pill-gut health connection. That’s one pill that’s easy to swallow.

Turns out, all guts aren’t created equal. Here’s how to find out what type you have. And these are the 5 surprising clues that your hormones might be out of whack.