The Startling Ways that Birth Control May Impact Gut Health and lead to IBD

Medically reviewed by Amy Fathman, DNP, FNP-BC

Over the last year, I was diagnosed with polycystic ovary syndrome (PCOS) and began working to balance my hormones through diet and lifestyle changes. My personal experience with the Autoimmune Protocol (AIP) diet aligned with recent studies suggesting that an anti-inflammatory diet can mitigate the symptoms of both PCOS and gut dysbiosis—an imbalance in the microorganisms living in your digestive system that can cause a host of GI symptoms.  

By all accounts, I am not alone in my gut-related symptoms. While my digestive complaints were not severe enough to warrant a clinical diagnosis, studies show that cases of inflammatory bowel diseases (IBD), an umbrella term for disorders involving chronic inflammation of the gastrointestinal tract, are rising rapidly worldwide. Symptoms of IBD can include nausea, vomiting, diarrhea, cramping, bloating, and abdominal pain, among others.  

While researching the risk factors for IBD, I was surprised to learn that a genetic predisposition can account for less than 25% of cases. Scientists now believe that external, environmental factors may account for much of the remaining 75%. What shocked me most was learning that oral contraceptives have been clearly and consistently associated with an increased risk for IBD since at least 2008, with case reports stretching back to the 1960s. 

The connection between the pill and IBD 

In fact, the number of studies suggesting that oral contraceptives negatively impact gut health grows each year, and known side effects of hormonal birth control include GI issues like nausea and upset stomach. The association was first suggested through case reports that appeared in the 1960s and 1970s. Then, in 1984, one study showed that oral birth control use was common in 100 consecutive women attending follow-up clinics for IBD. Other studies demonstrated that symptoms of IBD often resolved when patients discontinued oral contraceptive use.  

A 2008 meta-analysis published in Gastroenterology, which combined the results of 14 different studies including a total of 75,815 patients, found that those using oral contraceptives had a nearly 50% increased risk of developing IBD. Dr. Hamed Khalili, a Harvard-trained gastroenterologist at Massachusetts General Hospital, headed a sweeping 2013 prospective study involving over 200,000 women that suggested that “oral contraceptive use was associated with risk of Crohn’s disease [a type of IBD].” Shockingly, the study specified that oral contraceptive use could triple the risk of Crohn’s disease in women with a family history of the condition.  

More recently, a 2017 meta-analysis of twenty studies and multiple databases reported that those exposed to oral birth control had a 30 percent increased risk for the development of IBD. Specifically, the studies showed that those exposed to birth control had a 24 percent higher risk for developing Crohn’s disease and a 30 percent higher risk for developing ulcerative colitis.  

Why a “leaky” gut is an unhealthy gut 

At this point, you might be wondering what birth control pills and the hormones they contain could possibly have to do with your digestive system—and if you yourself might be at risk for IBD if you are on or have ever taken birth control.

First, it’s important to understand that the gut microbiome is composed of the “flora” or microbes lining your digestive tract, and that these bacteria and viruses have a large impact on our overall health. For example, we rely on our intestines to form a tight barrier and keep harmful microbes out of our bloodstream. Sometimes, however, gaps form. When this intestinal permeability develops, a phenomenon sometimes called “leaky gut,” invaders may squeeze between the cracks. These harmful microbes may trigger inflammation and changes in our gut flora.

Furthermore, increased intestinal permeability is known to play a role in gastrointestinal conditions including celiac disease, irritable bowel syndrome, Crohn’s disease, and ulcerative colitis.  

Why oral estrogen might lead to a leaky gut 

In a 2016 article, Dr. Khalili points to two biological mechanisms through which birth control might harm gut health. First, he notes that oral estrogen is known to negatively impact gut flora. Oral estrogen, of course, is one of two main hormones found in birth control pills. When a woman is prescribed oral contraceptives, she is usually given a combination of the synthetic versions of two key female sex hormones: estrogen (estradiol) and progestin. The two hormones work together to hinder ovulation, thereby preventing conception. In addition, they make cervical mucus inhospitable to sperm, and change the uterine lining so that an embryo would be unable to implant should breakthrough ovulation occur and fertilization happen.  

Intestinal permeability appears to be another, unintended consequence of the hormonal changes wrought by birth control. Dr. Khalili cites experimental data from two studies suggesting that estrogen helps maintain the function of the intestinal barrier. He also writes, in no uncertain terms, that oral estrogen “has been shown to modify intestinal permeability,” and that intestinal permeability is “a critical step in the pathophysiology of inflammatory bowel disease.” In other words, oral birth control may lead to leaky gut, and a leaky gut may lead to IBD. If this is the case, then we have a clear indication of how oral birth control is detrimental to gut health.  

Similarly, Dr. Jolene Brighten, a naturopathic physician and leader in alerting women to the realities of post-birth control syndrome, emphasizes in one article that birth control can lead not only to leaky gut, but to “yeast overgrowth (candida), decreased microbial diversity and altered gut motility.” In fact, the problems birth control causes in the gut are the subject of an entire chapter in Dr. Brighten’s popular book about hormones, Beyond the Pill

Strategies for improving gut health 

If you’re suffering from IBD or compromised gut health, there is hope. The five strategies I outline in this article have been shown to help restore the gut microbiome, no matter how that dysbiosis occurred. Those approaches include incorporating probiotic and prebiotic foods into your diet, reducing your intake of sugar and processed foods, and switching out make-up and household products that contain potentially harmful ingredients. In a future article, I will offer more in-depth suggestions for how women exposed to oral birth control can intentionally heal their gut and restore healthy flora. If you’d like to learn more about the documented side effects of birth control, you can find a wealth of information here. It’s time to pay attention to the growing body of scientific literature showing that birth control is harming our health.

Additional Reading:

The Surprising Connections Between PCOS, Dysbiosis, and Gut Health

The Crohn’s-Birth Control Connection: More Gut-Wrenching News About Contraceptives

Is the Pill wrecking your gut?

How a Fertility Awareness Method Led Me to the Autoimmune Protocol

How an Anti-inflammatory Diet Can Help Balance Hormones

Why It’s Important to Trust Your Intuition When It Comes to Your Health

Insulin Resistance, PCOS, and Fertility Health: Are you at risk?


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