Hormonal Birth Control and Autoimmune Disease

Hormonal Birth Control and Autoimmune Disease

My Story 

I am a childbirth doula and that has led me to become well versed in the issues that affect women, especially young women, on a daily basis. A doula is not a medical professional or someone who can make medical recommendations, but rather someone who is well versed in current research, evidenced based practice, and can point people in the direction of research and resources that they may find useful and helpful in making personal decisions. It is this mindset, combined with my own personal health journey and experiences that has led me to write this post on hormonal birth control (HBC) and autoimmune disease.

My journey with HBC began in eighth grade when I began to experience severe and unexplained abdominal pain on a daily basis. Many times each day I would be overcome by a contraction-like pain that would originate in my sides and back and would wrap around to my front and build to an excruciating level before dissipating about 2 minutes later. The pain would cause me to turn completely white and feel nauseated and light headed. However, it happened so frequently that I learned to just work through it so that no one would notice. This, partnered with frequent dull pain localized in the lower right quadrant of my abdomen became a regular and concerning experience. I went to the ER for an appendicitis more times than I can count and each time they would send me home without a diagnosis but the assumption that the pain was gynecological in nature. Shortly after the pain began, my mom took me to a friendly female OB/GYN who diagnosed me with suspected endometriosis. I was put on a birth control bill that suppressed all but four cycles a year and told that they would monitor it. The pain never really went away, but I kind of liked only having four periods a year and I was not in a place in life where I ever thought to question a diagnosis or a doctor’s advice. This went on for about 3 years when, in my junior year of high school, I agreed to an exploratory laparoscopy to have the long suspected endometriosis fully diagnosed and hopefully removed. I went to the hospital, went to sleep and fully expected to wake up to a full endometrial report. Instead, I woke up to my mom’s voice telling me that they hadn’t found anything. For three years I had lived with a completely unfounded diagnosis and now I was lying in a hospital bed for absolutely no reason. I was understandably frustrated but after three years it was fairly easy to just pick up and carry on. At this point, I was so used to being on HBC that I decided to just stay on it after the surgery. That was until about 6 months later.

Hormonal Birth Control and Autoimmune Disease

Seemingly out of nowhere I started experiencing severe insomnia, anxiety, upsetting dreams, and feelings of emotional detachment. For a few months I kept these symptoms to myself hoping that they would just go away, but before long I began feeling increasingly depressed and detached and I told my mother how I was feeling. As someone who had never tolerated HBC well, she immediately identified my symptoms as HBC side effects and within days of stopping the pill I was feeling normal again.

After that experience, I stayed off of HBC for about a year and half but because my health was so poor that my hormones remained unbalanced and I dealt with terrible PMS symptoms, ovulation symptoms, and miserable periods. I felt like I was constantly at the mercy of my hormones. Hopeless, I decided to go back on the pill but unlike my early days of HBC use I reacted negatively to every single brand I tried. Some brought back my negative emotional symptoms, one brand made my hands shake constantly, others made me feel physically ill… the list went on and on.

Now through college and with my UC diagnosis, my abdominal pain had resolved and I was preparing to get married and needed to start looking at HBC for its intended purpose rather than just as the hormonal support supplement I had used it for up to that point. I had given up on the pill at this point, but I was still very young and unprepared to have children so I decided to try the Mirena IUD. I liked its reported high level effectiveness and I hoped that having the hormones secreted locally in the uterus rather than having to be digested and absorbed systemically would minimize the side effects.

For about a year I was happy. I had no visible side effects, I wasn’t getting pregnant, and my cycle was super light and short. However, after about a year I started to get painful ovarian cysts almost every month, then I started getting severe breast pain for two weeks out of every month and finally my hair started to fall out. Around that same time I kept running across horror stories of people experiencing seizures, tanking progesterone levels and infertility as a result of the Mirena. I have no idea if any of those stories were true or not, but I had begun AIP at the time and I knew that I would forever live with guilt if I experienced a life changing side effect from the Mirena that I could have prevented. I was still not in a place of being able to support a child so I wanted something that was still highly effective, my husband and I were still in the midst of graduate school craziness so NFP (Natural family planning) was not something that either of us could handle learning about or investing in. After doing my research, I decided to get a non-hormonal copper IUD. I have had it for almost a year now and I love it. It works perfectly for my life, I have had no side effects, and in fact through my diet and lifestyle changes my hormones have been able to balance out naturally. I was recently told by my integrative health doctor after a hormone panel that my levels are “perfect”. I am very happy with my decision, but it is just that MY decision. I know that this is a very personal decision so, here are some points about HBC and autoimmune disease pulled from recent research as well as a list of non-hormonal birth control options to consider.

Research Points

  • Sex hormones play a large role in regulating the immune system, which make them an important part of managing autoimmune disease (Dr. Sarah Ballantyne)
  • Using HBC and artificially altering sex hormones can make it more difficult to manage autoimmune disease (Dr. Sarah Ballantyne)
  • HBC depletes many vital nutrients including zinc and many of the B vitamins, which in turn weakens the immune system. (Chris Kresser)
  • HBC alters that state of the gut microflora increasing the likelihood of leaky gut, inflammation, gut dysbosis, and can even effect the gut microflora of future children. (Dr. Natasha Campbell McBride and Chris Kresser)

For information on recovering from long term HBC use check out this source

Non-Hormonal Birth Control Options

Copper Paragard IUD: more than 99% effective, not dependent on correct use. Lasts for 10 years or more. Works by disrupting sperm and secreting copper into the uterus which affects implantation. Best for women who want to avoid pregnancy for an extended period of time. Must be put in by a health care provider. Does not protect against STIs.

NFP (Natural Family Planning): 80-98% effective depending on correct use. This is a great options for couples in a long term, monogamous relationship who are comfortable with the efficacy rate and are willing to work together to communicate and plan ahead. It is also best used when a woman has a predictable 28 day cycle. Does not protect against STIs.

Male Condoms: 85-95% effective depending on correct use. Easy to access, does not require a health care provider. Does protect against STIs.

Diaphragm: 86-94% effective depending on use. Does not protect against STIs. Good for a woman who does not want to rely on condoms and is comfortable with the efficacy rate. Must be fitted by a doctor.


Jesse St. Jean

Jesse St. Jean

I am many things: a wife, a daughter, a sister, a nutritional therapist, a dog-mom… and I’m an autoimmune warrior.


  • Hello Samatha. I’ve been following your blog for awhile. You’re post are always great and very helpful. This one really hit home for me. I have been living with undiagnosed endo for 20+ years and have been on HBC for almost that long to control it. I’m not on HBC for any other reason. It has helped but endo pain is still present. How are you addressing the endo/abdominal pain now? Was it just treating the UC that resolved the pain? Is the Copper P-IUC addressing your endo pain? How did you normalize your hormones after going off HBC? I’ve been on AIP for 1 1/2 years to address multiple autoimmune issues. AIP diet and lifestyle has help me to almost 80%. I think the “endo” and continued HBC use might be one of the missing pieces of my puzzle but I’m confuse about what to do. I must have seen over 20 different doctors over the years and they all just want to put me on HBC. Any additional information or advice would be wonderful. Thank you very much.

    • Hi Meredith! Thank you for your comment. I do not have endo. as the doctors originally thought. My abdominal pain ended up being a result of my UC, so as I changed my diet and got the inflammation down The abdominal pain went away. The copper IUD will not do anything to immediately address true endo related pain because it is not altering the hormones or your cycle in any way. In regards to normalizing my hormones, I continued to follow the autoimmune protocol closely and I worked hard to address my circadian rhythms though sleep and stress management and I thick that that helped a lot as well, but it has taken most of this year for me to see the change in my hormones/PMS/ovarian cysts… Many people with endo aren’t able to 100% resolve it through diet and lifestyle and do require laproscopic surgery to remove the edometrial tissue but then they heal much more easily following the surgery and are able to avoid more long term problems because of the AIP diet and lifestyle. Angie over Autoimmune Paleo has had endometriosis and had surgery recently to help resolve it so she is a wonderful AIP resource. Without knowing more about your specific circumstance I think it is probably in your best interest to talk with your doctor and try and confirm whether or not you do have endo so that you can make an informed decision on how to proceed. Good Luck, I hope you a re able to find full healing soon!

  • After six years of HBC and multiple autoimmune issues I got a paragard last month too! So far I am loving mine as well. I’m glad to read that you are having a good experience with it. Good luck and I hope it continues to work for you! By the way….my sister had a bad experience with Mirena too (though not as severe as yours). Hormone free is the way to go!

  • Samantha, great post! It seems this is not frequently addressed in the community but definitely needs to be. I, like you, tried endless hormonal methods for over eight years in effort to help with various health issues but I always ended up a wreck physically and emotionally – Mirena being by far the worst. Anyhow, I’ve been using the Paragard for birth control over two years now and would not trade it for anything! It may not be for everyone, but I absolutely love it and the freedom from hormones and worry it provides. However I am curious to see if any studies have been done on if it is more likely to negatively affect those with AI disorders given that physiologically we’re more prone to inflammation in general – even living the healthiest lifestyle we can. Have you heard or seen anything in regards to that?

    • Hi Holly,
      If you are asking specifically about the paragard, I have not seen anything that specific. The only thing I have seen regarding the paragard is that it can be a problem for some people who have trouble metabolizing copper or have an imbalance between copper and zinc. This may be a problem that some AI people face just because having inflammation can do damage to the body that can mess with your absorption, but I only saw one fairly unreliable study on that a long time ago and it looks to me like the rates of that happening are very low. However, if you are concerned about it I would consider talking with your doctor about taking a zinc supplement as that would likely help the problem.

  • I appreciate you sharing your story! I think more women need to talk about both the immediate side effects and the long-term consequences of birth control. I took HBC for over ten years and regret it. If I only knew then what I know now! I think it made my Hashimoto’s worse as well as fueled the growth of my uterine fibroids, which I had removed surgically last year. I recently wrote about my story with The Pill too. It looks like you and I have come to similar conclusions, even if we have used different ways to manage our hormones naturally. I have used natural progesterone cream. http://restoredroots.com/3-drugs-that-ruined-my-health-part-2-birth-control-pills/

  • Just an FYI, NFP is not “best” used when you have a predictable 28-day cycle. Sure, that makes it easier to learn in the beginning, but NFP is actually a great practice for those with irregular cycles and/or those with cycle issues. With the help of a doctor, NFP/tracking can even help to diagnose gynecological problems.

    • I have to second this! I have a history of very irregular cycles and have used NFP for both reproductive health issues (my NaPro doctor was able to diagnose me with endomteriosis and PCOS from 3 mos worth of charting, later I was able to put it into remission) and as family planning, and it’s worked fabulous for us.

  • I have known too many women who have gotten copper toxicity from copper IUDs. 🙁 Copper toxicity will disrupt all hormones (reproductive, thyroid, adrenal) and more. There’s a Pyroluria group on Facebook with good info.

  • Thank you so much for this article! I was diagnosed with UC about 4 months after I began taking birth control pills. Since then I have also been diagnosed with rheumatoid arthritis. I never associated my autoimmune symptoms with taking birth control but this article has brought some interesting concepts to my attention. I have been off of birth control for about 2 months now and am interested to see how this will affect me. Thanks again!

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Nutritional therapist Jesse

Hi, I'm Jesse

I empower women autoimmune warriors to reclaim their health by teaching each woman how to make the right food choices to heal her body while confidently owning her journey so she can live a vibrant life with chronic illness.


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