Birth Control and Gut Health

Hormonal birth control such as oral contraceptives, has been generally recorded as safehowever women who are prescribed it are seldom told of any potential risks associated with it. There is information that all women should know about, so that they can make an informed choice when taking it.

For my clients who have unresolved digestive issues or weight-loss resistance, we often make progress only so far until we come down to one missing link – hormonal birth control.


Studies have shown that oral contraceptives negatively impact gut flora and estrogen metabolism. This can lead to weight-loss resistance, increased risk of inflammatory bowel disease, depression and anxiety, and unresolved digestive issues.

A study of over 75,000 women found that those on oral contraceptives had an increased risk of developing both Crohn’s Disease and Ulcerative Colitis. Oral contraceptives, irrespective of the specific formulation, are associated with a 60% increase in endogenous estrogen and a 2-3 fold increase in sex-hormone binding globulin (SHBG).

Oral estrogen has been shown to impact our gut flora in negative ways, making us more susceptible to intestinal permeability (aka leaky gut). This is where the lining of the small intestine becomes damaged and undigested food particles, bacteria and toxins leak through the intestines into the bloodstream. This can present as:

  • Bloating
  • Diarrhea
  • Headaches
  • Abdominal pain
  • Mental fog
  • Constipation
  • Acne
  • Indigestion
  • Acid reflux

This can lead to poor nutrient absorption, food sensitivities, skin conditions like eczema or rosacea, or more serious concerns such as thyroid issues or inflammatory bowel disease.


The liver is the primary organ responsible for detoxification in the body, and birth control pills can affect the liver’s ability to process certain substances.

Specifically, oral contraceptives contain synthetic hormones, such as estrogen and progestin, that are metabolized by the liver. The liver breaks down these hormones and removes them from the body. However, birth control pills can increase the liver’s workload and affect its ability to process other substances, such as drugs, alcohol, and environmental toxins. This can lead to an increased risk of liver damage and other health problems.

In addition, oral contraceptives can also affect the levels of certain nutrients in the body that are essential for detoxification, such as B vitamins, magnesium, and zinc. These nutrients are necessary for proper liver function and detoxification processes.

It’s important to note that the extent to which oral contraceptives affect detoxification processes varies among individuals and depends on a variety of factors, such as the specific type of birth control pill, dosage, and duration of use. It’s always a good idea to talk to your healthcare provider about any concerns you may have about detoxification while taking birth control pills. They can advise you on ways to support liver health and proper detoxification, such as eating a healthy diet, staying hydrated, and avoiding alcohol and environmental toxins.

If you decide to stay on the pill

Taking oral contraceptives is a personal choice. The purpose of this article is to create awareness of the potential negative side effects. I was on them for 9 years and it exacerbated my chronic gut issues. If you are prescribed an oral contraceptive for reasons other than preventing pregnancy, it is important to explore and address the root cause of why a doctor might be prescribing it.

Birth control can affect the body’s absorption, utilization, and storage of certain nutrients. Some of the nutrients that may be depleted by birth control include:

  1. B vitamins: Birth control pills may interfere with the body’s absorption of B vitamins, including vitamin B2, B6, and B12. These vitamins are essential for maintaining healthy nerves, red blood cells, and energy production.
  2. Magnesium: Birth control pills may deplete magnesium levels in the body, which is essential for maintaining healthy bones, nerves, and muscles.
  3. Zinc: Birth control pills may also interfere with the body’s absorption of zinc, which is essential for a healthy immune system, wound healing, and healthy skin.
  4. Vitamin C: Birth control pills may decrease the levels of vitamin C in the body, which is a powerful antioxidant and essential for maintaining healthy skin, cartilage, and blood vessels.
  5. Folate: Birth control pills may interfere with the body’s utilization of folate, which is essential for DNA synthesis, healthy red blood cells, and fetal development during pregnancy.

This is why I have clients who are on birth control take a high quality multivitamin in addition to focusing on supporting liver health.

For a great resource on this topic check out Beyond The Pill by Dr. Jolene Brighton.

In great health,


Published On: January 25, 2020Categories: Gut Health, Supplements

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10 months ago

This information should be discussed as a side affect when being prescribed. I only recently learned about the impact on gut health. Is gut microbiota impacted by other forms of hormonal contraception, such as nuvaring, the shot, implant? I cannot find anything about how the ring impacts gut bacteria.

Thank you!!

2 years ago

Thank you so much for this post. I had a laparoscopic excision to remove adhesions off my bowels. After that (10 months ago) I formed SIBO and the inability to defecate. I resolved the SIBO issues – an ongoing process – which gave me my motility back but I coincidentally stopped the birth control that I was taking continuously to skip my periods. I could feel my natural hormones trying to overcome the birth control so I gave in and allowed myself to have a period. Just like that, completely normal ability to have poops again. Could this be from the pill?

2 years ago

I’ve been having very bad digestive/ bowel issues for the past 3 years. Within those 3 I’ve been on the pill and have been in a relationship. My digestive issues before were from stress/ anxiety but never happened as often. Now it’s too way too often. So often it’s inconvenient and of course that stresses me out more and gives me anxiety from possibly eating something that will ruin the rest of the day. Vicious cycle. Reading this really made things click. And me make my decision to stop taking my birth control as well so I can have my life back without worrying about where the closest restroom is as soon as I’m done eating.

Erin B.
3 years ago

This is fascinating information! I have struggled with digestive issues for 2 decades, which coincide exactly with the amount of time I’ve been taking birth control pills. This is all the motivation I need to finally stop using them and see if I can finally fix my digestive issues! THANK YOU!