The Truth About Birth Control Pills and Hormones

woman and birth control pills

“The pill” is one of the most popular forms of birth control in the world. Statistics show that in the U.S., approximately 1 in 4 women aged 15-44 who are using contraception are taking oral contraceptives, also known as birth control pills. What many of these women don’t know is that the birth control pill can cause an imbalance of hormones, which have negative impacts on brain function and mental health.

In fact, many women have misconceptions about how these hormonal contraceptives affect the brain and body and how they influence overall health. It’s time to clear up the confusion.

Research shows that taking birth control pills causes structural changes in the brain, alters neurotransmitter function, and messes with mood regulation. Click To Tweet


Oral contraceptives are most commonly associated with preventing pregnancy. However, they are also frequently used to reduce symptoms that may occur with menstruation, such as:

  • Irregular periods
  • Premenstrual syndrome (PMS)
  • Premenstrual dysphoric disorder (PDD)
  • Pain and cramping
  • Heavy flow
  • Endometriosis
  • Polycystic ovarian syndrome (PCOS)
  • Fibroids

Because the pill can effectively decrease symptoms of these conditions, it is commonly prescribed.


Most oral contraceptives are made with combinations of synthetic estrogen and progestin, a synthetic form of the hormone progesterone. After taking the pill, these synthetic hormones enter the brain and act as endocrine disruptors, interfering with the signaling process that is necessary for ovulation.

In particular, they prevent the hypothalamus from signaling to the pituitary gland (which regulates your hormones) to secrete the hormones that cause an egg to be released. In the unlikely event ovulation does occur and an egg is fertilized, the synthetic progestin thins the uterine lining, making it more likely that the egg will be shed.

Many birth control pills include a week of placebo pills that induce monthly breakthrough bleeding, but this is not a real menstrual period. It is an artificial pattern that eliminates the natural ebb and flow of estrogen and progesterone throughout the cycle.


In order to feel happy and healthy, you need to have balanced hormones. Here is some important information to note about the differences between natural and synthetic hormones.

Natural hormones bind to specific receptors and keep your body in balance:

  • Estrogen binds to the estrogen receptor.
  • Progesterone binds to the progesterone receptor.
  • Testosterone binds to the testosterone receptor (yes, women produce testosterone, just not as much as men).
  • There is no cross-reactivity.

 Synthetic progesterone (progestins) acts differently on the body:

  • Progestins do not limit binding to just the progesterone receptor, rather, they bind to many other receptors as well.
  • When a synthetic hormone binds to the wrong receptor, that receptor may convey inaccurate signals, which throws the body off balance.

Because synthetic hormones may bind to the wrong receptors, birth control pills may cause hormonal imbalances and detrimental side effects. Not all women experience these problems, but for those that do, side effects can be quite miserable.


You may already know that birth control pills have been shown to cause problems with blood pressure. They also increase the risk of blood clots and strokes, especially if you smoke or have a history of migraine headaches. But did you know that birth control pills also affect your brain and mental health?

Research shows that taking birth control pills causes structural changes in the brain, alters neurotransmitter function, and messes with mood regulation.

  • Brain structure: A 2019 study found that the hypothalamus in women taking oral contraceptives was about 6% smaller than in women who weren’t on the pill.
  • Neurotransmitters and moods: Scientists from Denmark found that women ages 15-34 taking oral contraceptives were 23% more likely to start taking antidepressants for the first time than those who weren’t taking the pill. In fact, bouts of depression have been reported by 16%-56% of women taking the pill, which depletes the neurotransmitter serotonin.
  • Other neurohormones: Birth control pills also elevate cortisol levels (hello, stress!) and lower testosterone levels (goodbye, sex drive!). And low-testosterone problems can remain even after stopping oral contraceptives, putting you at increased risk for long-term sexual, brain health, and mental health disorders.
  • Microbiome disruption: Synthetic birth control can also disrupt the gut microbiome.

The gut—your gastrointestinal tract (GI)—is often called the second brain because it is lined with about 100 million neurons. That’s more neurons than you have in your spinal cord or in your peripheral nervous system.

Research shows that gut health problems, such as leaky gut, are associated with mood and anxiety disorders. A 2017 article explored the connection between gut health and ADD/ADHD.

  • Micronutrient depletion: Birth control pills interfere with the absorption of essential vitamins and minerals, which can lead to nutritional deficiencies, according to a 2013 study.

In particular, key nutrient depletions have been seen in folic acid, B vitamins (B2, B6, and B12), vitamins C and E, and the minerals magnesium, zinc, and selenium—micronutrients that are important for healthy brain function. If you’re taking oral contraceptives, it’s a good idea to take nutritional supplements to avoid deficiencies.


Many women have no idea that their birth control pills may be causing the following issues:

To find out if your birth control pills are contributing to your symptoms, it’s important to get tested. However, simple standard blood tests will rarely detect this problem.

A better option is a 24-hour urine hormone collection, which is the gold standard for looking at all the hormones and their metabolic byproducts. An integrative medicine physician, also called a function medicine physician, can be helpful in assessing hormone levels, nutrient deficiencies, and other issues related to hormonal birth control.


Going off the pill isn’t necessarily a quick-fix solution. Some women experience a rash of symptoms—including mood swings, anxiety, and depression—in the months following cessation of hormonal birth control. Some hormonal experts have started calling this effect “post-birth control syndrome.”

In addition, it’s important to remember that if you started taking the pill because you were experiencing irregular periods, fibroids, endometriosis, or other symptoms, the pill doesn’t actually address those issues. It only masks the problem. When you stop taking oral contraceptives, that original issue may return with a vengeance.

If you were experiencing menstrual Irregularities, take note that taking natural progesterone can be quite effective for some women—without any of the side effects of synthetic progestin in hormonal contraceptives.

If you’re concerned about unplanned pregnancy, there are other non-synthetic, non-hormonal birth control options available that you can discuss with an integrative physician.


If you have been taking birth control pills for many years, it can take several months to rebalance your natural hormone levels. This is due to the chronic suppression of your own hormone production. It is often helpful to supplement hormones during this recovery period.

If you must stay on the pill for any particular reason, consider asking your physician about using natural progesterone and/or testosterone to improve quality-of-life issues while taking the pill.

Depression, anxiety, and other issues related to hormonal imbalances can’t wait. At Amen Clinics, we’re here for you. We offer in-clinic brain scanning and appointments, as well as mental telehealth, clinical evaluations, and therapy for adults, teens, children, and couples. Find out more by speaking to a specialist today at 888-288-9834 or visit our contact page here.



  1. Spot on with this write-up, I absolutely feel this site needs far more attention. I’ll probably be returning to read through
    more, thanks for the information!

    Comment by Xmas Wishes For Mother & Father — December 1, 2017 @ 2:01 PM

  2. Glad to see Amen Clinics addresses the role hormones play in mood, memory, anxiety etc. Menopausal women are said to have ADHD symptoms. Is more than just a coincidence? I hope you are looking into this.

    Comment by pcombs — December 3, 2017 @ 11:37 AM

  3. Is it expensive? Will my insurance cover any of the hormone replacement?

    Comment by Rhea — December 4, 2017 @ 6:11 AM

  4. Thank you for covering this topic, as hormone imbalances are the origin of many neurochemical imbalances, especially in women. It would be very helpful if you further explored (in detail)this topic to include the major hormones that affect cognitive and emotional wellbeing. For example, Estrogen gets a bad rap from so many health publications yet it influences many biological processes that are essential to cognitive, emotional,& personality stability. (and the liver’s ability to process it) It is the Xenoestrogens in our environment that are wreaking havoc. Much of the research out there does not differentiate natural vs. bioidentical as you did in your article. It is also interesting that the depression rate is statistically higher for women than men… looking forward to further articles!

    Comment by Robbie — December 4, 2017 @ 7:11 AM

  5. What do you recommend for my daughter (19 years old) who suffers from moderate to severe cramps each month, PMS symptoms like irritability, mild depression/sadness, and just feeling miserable for about a week or more….?

    Comment by Susan Davila — December 4, 2017 @ 8:19 AM

  6. Most Synthetic BCP’s are also classified as Class 1 carcinogens by FDA … wish that was a required disclosure before I polluted my body for 20 years …

    Comment by Teresa — December 4, 2017 @ 8:45 AM

  7. As a Nutrition and Wellness Coach, I find this to be the most confusing topic for my clients. Foods are also related. Hormonal imbalances are related to many issues with mood and fatigue. How can someone get these hormone tests?
    I would love to learn more from Dr. Amen as he is my trusted “go-to” doctor! Kim Porcelli

    Comment by Kim Porcelli, Nutrition and Healing Coach — December 4, 2017 @ 9:02 AM

  8. My transgender teen son takes depoprovera to halt menses. He has gained a huge amount of weight and is now sluggish and depressed. Can natural progesterone work for this purpose?? Are there any suppliments or any other way to combat the unwanted side effects?

    Comment by So — December 4, 2017 @ 9:39 AM

  9. Great article. Women need to know that birth control pills do not “regulate” anything- they essentially turn off a cycle when actually what a woman needs is smart medical care to help figure out the underlying reasons her hormones are imbalanced to begin with.

    Comment by Ellen — December 4, 2017 @ 11:53 AM

  10. Is hrt that you are using same as other clinics that are using as bcp?

    Comment by Miae lee — December 4, 2017 @ 12:30 PM

  11. I mean bio identical hormon. Not bcp

    Comment by Miae lee — December 4, 2017 @ 12:31 PM

  12. What about post menopause women ? How to balance hormones after 50 and increase libido ?

    Comment by margaret Lehnert — December 4, 2017 @ 2:00 PM

  13. Please help with more of woman’s hormonal balancing issues if possible in the future, I do not think that people are aware that your clinic even offers this as an option.
    It is especially important for woman with PMS.induced mood & depression issues. as well as pre and Menopausal issues….Even after a woman gives birth too.

    I feel that after having a Thyroid Crisis-Hashymotos Thyroidosis, at age 41, I could have benefited from this sort of complementary Interventional Medicine…I had night sweats so bad, insomnia/Low Cortisol in AM/Afternoon hrs, and now I have at 57 going on my second hip replacement soon….My mother also has had the same progression too. I have had adrenal fatigue for years as well, and supplement it with a brand of herbs…Your formulas have helped a great deal with stress, anxiety, and insomnia for me. I only wish I could have had the Natro-pathic advice from your clinic at the time I was perimenopausal. Thanks Cheryl

    Comment by cheryl ku — December 4, 2017 @ 7:17 PM

  14. Ꮶeeр this going please, great job!

    Comment by blend — December 6, 2017 @ 3:54 AM

  15. Absolutely I feel that I have developed ADHD and many other mood and memory issues as I go through menopause. Would love to get more solid reliable information on how best to deal with this situation for the long term.

    Comment by Alana — December 18, 2017 @ 7:31 AM

  16. Hi.I just wanna know if what contraceptive pill is the very best and effective one? Then after a month of taking it i will get pregnant easily?

    Comment by Emma — December 23, 2017 @ 9:20 PM

  17. Great information

    Comment by Fatima — January 29, 2018 @ 6:17 AM

  18. Bioidentical progesterone would certainly be better than provera, but I’d have thought the best hormone replacement for a trans man would be testosterone. Depo Provera is nasty stuff, ignorant doctors sometimes give it to trans women, where it has a reputation for causing severe depression and suicides. In our HRT group, some of us have developed a theory that provera (and other progestins) cause depression and other adverse psychological effects by depleting neurosteroids (neurosteroids are steroid hormones produced in the brain, that have anti-anxiolytic, anti-seizure and antidepressant effects, stimulate neurogenesis, and just generally do stuff that keeps your brain and nervous system in good shape). Progestins are known to interfere with some of the key enzymes involved in neurosteroid synthesis (for instance 5 alpha reductase). Also, progesterone itself acts as a raw material from which one of the most important neurosteroids, allopregnanolone, is made. By mimicking the action of progesterone, progestins might be deceiving the body into thinking there’s more progesterone present than their actually is, causing it to downregulate progesterone production and leading to further depletion of allopregnanolone.

    Another effect of progestins is that they block the release of gonadotropins (LH and FSH), which has the effect of shutting down your sex hormone production (this is why progestins are often used as chemical castration agents for sex offenders). Some of the effects of sex hormone deficiency include weight gain, depression, and lack of energy.

    Comment by Hugh — February 3, 2018 @ 12:54 PM

  19. I’ve been taking Levora for years for testosterone-related cystic acne and since it helped only marginally, I went on Norgestimate, and it worked! It dried out my skin, a lot, but I also experienced weight gain and water retention. These side effects only got worse over time so I went off of it after 5 months and back on Levora. It’s been 9 months and these side effects still haven’t gone away. When I wake up in the morning, my stomach is smaller but right after drinking some room temp water, it gets bigger and stays bloated throughout the day no matter what I eat or drink. I tried dandelion pills but they gave me hives, as did hibiscus. I don’t know what else to do at this point. Any advice would be greatly appreciated.

    Comment by Blue — February 12, 2018 @ 2:42 AM

  20. Hi. I have my irregular mens for almost 8 mos. now. i am 43. It started when i was 41. My dr. Prescribe me Marvelon just today. For hw many months will i take this meds? I am just confuse. Thank u very much.

    Comment by Airon — March 27, 2018 @ 4:16 AM

  21. What is the possible side effects of this drugs. ?

    Comment by Airon — March 27, 2018 @ 4:26 AM

  22. Hello Airon, thank you for reaching out and sharing with us. To get more detail on your specific case and symptoms, please call our Care Coordinators at 888-288-9834 or submit this form on our website – Speaking with your primary care physician about current medications is recommended, and we can offer additional consultation to you.

    Comment by Amen Clinics — March 27, 2018 @ 8:43 AM

  23. My 18 yr old daughters have PMDD. They were both put on YAZ after diagnosis for many years. A recent dr switched my daughter to Nuvaring as it is “safer”. After a few weeks she went into deep treatment resistant depression that has lasted a year. She returned to YAZ immediately after the depression started but hasnt been able to get her pmdd or depression under control. No SSRI has helped- only makes it worse. At a loss and tired of switching providers & out of money….. help!

    Comment by Kaylyn — March 27, 2018 @ 7:34 PM

  24. So true!

    Comment by Momof4 — February 19, 2019 @ 7:47 AM

  25. I am unaware of any insurance that covers bio identical hormones. Hopefully, this will change in the near future, because there are many benefits of using Bio Identical hormones.

    Comment by Melanie Mitchell — February 20, 2019 @ 7:53 AM

  26. So frustrating that docs will not Rx even 0.01mg of estrogen even if you have ALL the symptoms unless they get a level on you first. But they will gladly almost force SSRIs on a menopausal woman, any woman w/o getting anything checked first.

    Comment by KJ — March 17, 2019 @ 7:13 PM

  27. So sad to see a woman get in a relationship she thinks will be long term so starts ‘the pill’. Next thing you know, she is acting all wacky and they split up. She goes off the pill and is ‘normal’ again. Then they think, mistakenly, its being in a relationship that makes them unstable.

    Comment by kj — March 17, 2019 @ 7:15 PM

  28. May I suggest Chinese herbs and/or acupuncture as well as evening primrose oil or fish oil, B6 and SAM-e. Sorry if that was unsolicited but I didn’t see a reply.

    Comment by kj — March 17, 2019 @ 7:18 PM

  29. I have no children and probably won’t have any at 41 years old now!!! I’m so frustrated here’s my issue and story.! Since turning 38-39 I noticed headaches fatigue weight gain irritation irregular periods starting. I went months and months one year bleeding almost every day that it put me anemic I didn’t know any better as to what

    Was going on?? I finally have been checked. Was told I had PCOS by one obgyn. He said he knew that by the way my hair on my low pelvic grew and then started testing me. Came back negative basics for all the things he thought. He did do a biopsy on my uterus to say yes it thickens and that’s what was causing my bleeding I wasn’t ovulating?

    So in order to stop my bleeding he put me on the Estrella. After starting that my periods or irregular bleeding from not ovulating did stop. I have been on them for a couple years now only issue is I can’t lose weight ha! andddd have severe headaches and irritation and fatigue etc when the 7 days of the pill is stopped! Estrella is the pill. Therefore I went to a new dr and told her all this i need something to replace the placebo pill days due to the severe drop in the hormones when I’m off of them for that 7 days and the cramps. She tried to put me on sesonique. Well second night of that I had hot sweats blood pressure issue severe what I believed to be reaction so I let her know I was super sick on that she had me stop that!! Mind I my insurance usually covers birth control.!!!
    Now she prescribed me Sejunel or something like that… well I go to get the two bags and one was expensive I can’t afford that every dang month for them placebo day replacements. Even if this did work I can’t afford it now!!!

    So i left her a message we need to find someone that my insurance covers. But mind U I’m now without anything my hormones are now dropping severely and I’m laying her with a headache and sickly feeling sick and she told me not to start the new pills tell next week!! Well hello know my history and the way I drop why wouldn’t she prescribe me something else now to hold me over I cant even function one day not having the hormones issues happen and she’s not ahead of the game I guess. I know there’s only so much they can do but I’m today’s day and age I would think there’s preparation in this!!!

    I just wanna be normal and have my hormones function like before but I guess that’s not happening.? We all want the best for ourselves. So now that I can’t afford the tapering pills I said what if o go back to the first pills I was originally on them things did make me feel normal again. She won’t do it she always it’s to much to put I back on.

    I said it can’t be any worse then how I’m feeling now ughhh I’m so frustrated!!!

    So now I gotta wait. I didn’t ask her why did she think my hormones are doing this at 41 is there a way to know why?? Like testing on hormones she said yes blood work on hormones. I said can I get labs done for this? Maybe that will reveal something as to why All this is going on… she just felt it wasn’t necessary for me to since I was responding fine for the first birth control. I’m like I understand that but ppl also would like to be off of bc sometime and find the underlying reasons to why they Have these imbalances. I get it’s a helpful solution for now but I do not want to be on pills for the rest of my life either like many others who try to be as natural as possible.

    So I’ll have labs done. But wouldn’t u think she would have said hey let’s test u? They never want to figure anything more out and depend soley on these pills . U really have to be you’re own advocate on this world.!!! Anyways I just took the first Sejunel or whatever it’s called to test it out because I can’t take this feeling of sickness I need something to make my hormones relax this is awful for anyone who ever has to go through this I pray you don’t… if there are any ideas or recommendations plz message me l. Not sure what else to do. Am I doing something wrong by not having normal hormones?? Am I at that age? Help!!! Ty in advance.

    Comment by Lisa — October 31, 2019 @ 5:58 AM

  30. So what I am getting out of this article, is that women who can get pregnant should stop taking birth control. Isn’t that bad advice.
    Look how many unwanted pregnancies we would have! Explain!!!

    Comment by Veronica Kohler — November 25, 2019 @ 10:20 AM

  31. Ladies, PLEASE be careful with any hormone replacement therapy…..even bio-identical hormones! I have had breast cancer twice and the second time, I realized that it was after I had been taking bio-identical hormones that the cancer developed. I then found out that I have SNP’s (Single Nucleotide Polymorphisms) in my COMT genes, which makes metabolizing Estrogen very difficult. I love what Dr. Amen and his colleagues are doing, but make sure to ask if they are first checking your genetic SNPs before taking any hormones. Please do your research and get your Genomic Profile looked at before taking Bio-identical hormones. Blessings to you all!

    Comment by Julie Goos — November 26, 2019 @ 10:31 AM

  32. Julie Goos, Spot On! Genomic profile isn’t part of the pre-prescribing protocol. I had to fight through insurance rejection even after breast cancer diagnosis. Great surgeon and oncologist getting it done. Generation X – cross us out… The most inadvertently poisoned generation ever. Thanking Dr. Amen for working to save us and our kids’ lives.

    Comment by Adrienne Addie — November 27, 2019 @ 2:55 AM

  33. What should I do! I’ve gained so much weight for the past 4 years. After taking two shots of depo my weight really went crazy, I did stop taking it for 1 month then started the IUD, stayed with it for 4 years, unfortunately my weight just spiked! I went from 149 lbs to 249 in 4 years! Through this period I’ve been on strike diets such as keto, exercising like crazy but seems like I keep gaining more weight! I’m only 25 and I feel depressed because of my weight! It’s sad that I’ve seen several doctors even nutritionist and none of them seem to help me! Is the any medication I should take? I’ve been taking vitamins such D and B complex but it doesn’t help also! I don’t like sugary foods or drinks, neither salt foods! My carbs intake is low due to an underline stomach discomfort! But still nothing seems to work for me! Please help me if you can

    Comment by Gabby — June 26, 2020 @ 12:55 PM

  34. It is a pleasure worth reading this article as it provides us information on practicing compassionate medicine.It is one of the best options to read from here in detail. I would go for this site even in future when needed. Great blog indeed, will visit again future to read more!!

    Comment by Vital Life Wellness — September 21, 2022 @ 2:18 AM

  35. Lovely article! I had a friend who tried to get me to take these pills due to painful periods, it was tempting but I decided to get help from a doctor that deals with natural medicine and trust me it works! Getting to the root cause was a blessing. Plus women who are trying to prevent pregnancy should try natural or alternative methods.

    Comment by Tricia — January 15, 2024 @ 12:06 PM

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