Do Estrogen and Progesterone’s Rise and Fall During Your Cycle Create Autoimmune Flares? (Yes, Unfortunately.)

Girlfriends having coffeeWhich hormones fluctuate throughout the month during my cycle – estrogen and progesterone, or just estrogen?

The menstrual cycle proceeds through a complicated and highly coordinated dance of hormones.  By convention the cycle begins with menstruation.  During this time, levels of estrogen and progesterone are low.  During the next part of the cycle, levels of estrogen begin to rise, reaching a peak around the time of ovulation.  After ovulation, levels of estrogen remain relatively high, dropping off in the days leading up to the start of a period.  Progesterone levels remain fairly low before ovulation, but then remain high, dropping off just before menstruation.  Other hormones change cyclically too (such as the ones triggering ovulation), but estrogen and progesterone are the hormones thought to be most important for premenstrual syndrome and possibly symptom flares in women with autoimmune disease.

If my autoimmune symptoms seem to get worse when these hormones are high or low, is this typical?

Not all women with autoimmune diseases note symptom changes with their menstrual cycle, but many do.  Sometimes it may be difficult to distinguish a pattern, since symptom exacerbations may be triggered by many other factors.  Many women with rheumatoid arthritis, for example, report decreased joint pain in the period right after ovulation, as well as during pregnancy—both times when levels of estrogens and progesterone are high.  These women may note increased symptoms when these hormone levels are particularly low, such as during menstruation or in the postpartum period.

One questionnaire found that 70% of women with multiple sclerosis noticed cyclical changes in their symptoms, with the worst symptoms in the week before the start of their period.

Women with lupus also often note symptom flares just before and during their periods.  There is not one specific pattern that applies to symptom flares in all types of autoimmune diseases, though within specific diseases there is often more of a pattern.

Have there been any research studies about why hormone level fluctuations throughout a monthly cycle can worsen autoimmune symptoms/create a flare?

More research needs to be done on the relationship between hormone levels and autoimmune symptoms.  It is well understood that steroid hormones, including estrogen and progesterone, influence the development of immune cells and modulate the output of the immune system.

Many immune cells have receptors for these hormones, including many of the immune cells responsible for creating autoimmunity.   It is not surprising, then, that variations in hormone levels during the menstrual cycle might lead to changes in symptom severity.

Certain hormones may tend to activate a certain part of the immune system (e.g., the TH1 response, which activates macrophages) while simultaneously tampering down another part of the immune response (e.g., the TH2 response, which promotes the activation of B cells).

Some hormones, such as estrogen, may enhance the immune response at low levels while generally inhibiting the immune response at very high levels.  Sex hormones also activate specific genes, some of which may play a role in symptoms flares or symptom reduction.

Many of details about this are still being worked out, however, and most of the work that has been completed has involved animal models of autoimmune diseases or simpler cellular systems.  It is a very complicated problem to study; in a human being, multiple levels of hormones are changing concurrently, each of which might have some effect on the activity of the immune system.

Could hormone therapy help regulate my hormones to assist with leveling out autoimmune symptoms?

It might.  It also might exacerbate your symptoms or have little effect.  At this time, there is not a general clinical recommendation supporting hormone therapy in autoimmune diseases.  Research on this is in a preliminary stage, and the amount of information available varies by disease type.  For example, current evidence suggests that postmenopausal women with rheumatoid arthritis who use estrogen therapy may have fewer symptoms.  Other clinical trials of postmenopausal women with lupus have found increased disease activity with estrogen therapy.

Research on premenopausal women is also in a preliminary stage, but some evidence suggests estrogen therapy may lead to decreased symptoms in multiple sclerosis; clinical trials are ongoing.

Questions for your doctor:

  • What (if anything) is known about whether birth control pills or other hormone therapy might help with symptom reduction in my particular autoimmune condition?
  • If am pregnant, is there anything I can do to help prevent a postpartum disease exacerbation?
  • If hormones are thought to exacerbate symptoms in my autoimmune condition, what other non-hormonal options for birth control are available?

Have you noticed that flares that are related to certain weeks in your cycle?  Share your experience below!


About the Author
Ruth J. Hickman, MD, is a freelance health, science, and medical writer.  She specializes in writing about medical topics for the lay public and for health science students.  She can be reached at [email protected] or through her website: ruthjhickmanmd.com.

This post contains opinions of the author.  AutoimmuneMom.com is not a medical practice and does not provide medical advice, diagnosis, or treatment.  It is your responsibility to seek diagnosis, treatment, and advice from qualified providers based on your condition and particular circumstances.  Camino Real Ventures, Inc., the company that makes AutoimmuneMom.com available to you, does not endorse nor recommend any products, practices, treatment methods, tests, physicians, service providers, procedures, clinical trials, opinions or information available on this website.  Your use of the website is subject to our Terms of Use and Privacy Policy


  1. Vicky Hughes says:

    Hi, I am a 37 year old female living in the UK.

    2 years ago I had a major postpartum haemorrhage, lost approx 8 litres of blood. I was heavily transfused. Since then, I have been increasingly unwell and have had to give up work.

    I have severe joint pain, which worsens when I ovulate, and seems to settle for a short while after my period. I am breathless and exhausted after just walking upstairs. I have a rapid heart rate, cold feet, headaches, repeat infections and hair loss. I have just had an MRI on my spine (they were looking for MS lesions) which shows I have hyperplastic vertebral marrow. I am seeing the haematologist on Monday coming, also waiting for referral to rheumatology.

    All my blood tests are fine, so it can’t be anemia or myloeddysplasia, which has been the suggestion by the hospital upon seeing my MRI.

    Would anyone have any ideas what is wrong with me? Getting desperate for some help and advice.

    • Amber Parker says:

      I have a story similar to yours αnd discovered I had an autoimmune disorder called POTS (Postural Orthostatic Tachycardia Syndrome). Have all your symptoms αnd more. Before I found out what I had, I thought I might have hypopituitarism, which is when your pituitary gland no longer provides the signals that your body needs in order to produce more secretions of hormones so they can be sent throughout your body. Therefore an imbalance of hormones αnd even some thyroid dysfunction is expected. This can happen after an extreme amount of blood loss, during the time of losing that blood, a small area of your pituitary gland experienced some tissue death of cells. Well, since this gland is the brain network of telling the body what hormones it needs, it’s like a bunch of static during the communication αnd these symptoms will follow. Do some research on this, hope it helps.

  2. Katie Cleary says:

    Hi Vicky,
    I’m sorry for the pain you’re going through and the lack of diagnosis. I hope the doctor appointment gave you some clarity. There is a Q&A section of this website, and I can also post your question on Facebook. The Facebook AutoimmuneMom community is pretty fast at answering questions, so that might be the quickest way — let me know if you are all right with me posting it and then I can get back to you with the answer or you can “like” the page and watch the answers as they come in! It’s up to you and I would post the question as an autoimmune mom friend so it won’t have your name etc.
    Thanks and take good care,

  3. Vicky Hughes says:

    Thank you so much, any help would be appreciated. I saw the haematologist yesterday, and they are not going to investigate the marrow problem, they as my blood tests are fine it was probably an incidental finding? Still waiting for rheumatology appointment.

    Please post on my behalf, maybe someone out there may have an idea what I can do next.

    Best wishes and thank you again, Vicky.

    • Katie Cleary says:

      Hi Vicky,

      Ok I posted this and I’m sorry it took me a while to pull all of the responses together to reply on this. Here were the ideas:

      -Have they checked thyroid levels including TSH and reverse T3?
      -Please have your thyroid tested thoroughly as all of your symptoms sound very thyroid related. Make sure they at minimum test your TSH, T4, T3, rT3, Free T4 and Free T3 and B12, Vit D, TIBC and ferritin and ANTIBODIES, not just the TSH and T4, that is a limited picture. All of your thyroid panel can be normal and yet all of your symptoms can be present with the autoimmune disorder itself. I know, I live it everyday. This article helps to explain what happens BEFORE the thyroid actually begins to fail. Hope this helps a bit.
      -Have you been checked for coeliac? Or Hashimoto’s?
      -I’ve been sick for years. Just found out it’s late stage Lyme’s disease. It could have come from your transfusion. I would find out if its a possibility.
      -Check for Babesia that could have been in the blood transfusions !
      -Had a similiar experience at about the same age. 25 years later they reviewed my history and decided it fit into the pattern of a blood disorder. Just remember if you have one autoammune disorderyou could have more. Hope you get answers soon.
      -My guess would have been Hashimoto’s and possibly adrenal fatigue with that. That’s how we with the disease feel — exhausted, headaches, hair loss, infections, all over body pain.
      -Thyroid Pharmacist, Dr Izzabella ? Here on facebook may be helpful
      -Definitely see a cardiologist. Rapid heart rate shows your heart is under stress. I have SLE and have had constrictive pericarditis
      -I’ve had adrenal fatigue and those are very similar symptoms. Biggest part of my treatment was good whole food brand vitamin c in larger doses to heal the adrenal gland. (Get a 24 hour saliva test)
      -Sounds like addisons
      -I have a condition called dysautonomia which gives me many of those symptoms , fatique , rapid heart rate etc. I have rapid heart rate while standing and anything else I do.

      As you can see there are a lot of ideas — I hope this helps rather than overwhelm. Don’t give up and thinking good thoughts for you on your quest to find the right doctor who will listen and give a diagnosis. Please keep us posted! xo, Katie

      • Vicky Hughes says:

        Well funnily enough Addison’s has been mentioned by the Haematologist, also Sheehans Syndrome, where your pituitary gland gets starved of blood during a post partum haemorrhage. My thyroid function is fine, everything they’ve tested so far is normal. I have not been tested for Lyme Disease, or a any other virus. Unfortunately, I do not have a supportive Doctor, and am at the mercy of the long NHS waiting times. I have to go back and see the Haematologist in 6 weeks when they will decide wether to discharge me from their care or transfer me to another department. So frustrating when you need answers and want to well for your children! I am touched by the responses and thank everyone for their comments.

        • Michelle says:

          Hi Vicky, did you get anywhere with the NHS at all? I have been struggling along for 2 years and my doctor refuses to refer me to a rheumatologist. Your symptoms sound very similar to mine. I just want to be well for my children too :(

  4. I’m 30 and have had Crohn’s Disease and related Arthritis for 21 years. I also have issues during low estrogen cycle times, mostly in the week leading up to my period. I’m currently TTC and having difficulty as I have a mini flare following the time when I should be ovulating and during the time I could be conceiving. I’m having difficulty, and I’m wondering if the flares are preventing me from conceiving. The first two weeks of my cycles I feel great, aside from the normal period cramps. Very frustrating.

  5. I am going to the doctor today. Its been just a few days under 4 years since I had my daughter and my life has been turned upside down by these auto immune flares. I haven’t been diagnosed yet but believe me I have tried. My veins and arteries get swollen and so painful. I also get arthritis symptoms or should I say swelling in my hands and feet and knees. These are just flare ups though and usually come on during my period. I also get fatigue extremely bad. Its usually one or the other symptom instead of both at the same time but they will come after each other. I hope I get help today and I hope the doctor listens.

    • Michelle says:

      Hi Sarah, I have the same vein symptoms. Mostly around ovulation or around my period. The doctor looks at me like I am stupid and says there is no such thing as vein pain. Some times they are visibly bulging on my hands. The fatigue is horrendous. Short on breath and I look like I have been dug up!
      Did you manage to get anywhere with a diagnosis?

  6. belinda Quardey says:

    Hi, I have been diagnosed with mixed connective tissue disease. I have noticed when the weather is warm I am relatively pain free but when there’s a change in weather especially when it’s cold I turn to have flare ups. Any suggestions as to how I can help myself when the situation gets bad ?

    • TAMMY HANCE says:

      hello, I have eds and I have been having a terrible time with menopause. I am 53 and no hot flashes, still have a period every 4 weeks. I just feel like I have the flu when I should be ovulating on the 12th day…..I ovulate on the 18th day now. or I get sick when I am having my period. I feel like im estrogen dominant… estr – 61… prog -1.7…test – 45….. fsh 54…lh 32….

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