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Autoimmune Hashimoto’s Flare-Ups and Your Menstrual Cycle

Do menstrual periods cause autoimmune flare-ups in patients with Hashimoto’s?
Autoimmune Hashimoto’s Flare-Ups and Your Menstrual Cycle
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It’s that time of the month again. You’re feeling cranky, bloated, and suffering from cramps – all signs that “Aunt Flo” is on the way and your period will arrive soon. Menstrual symptoms are bad enough in many cases, but if you have autoimmune Hashimoto’s disease, should you also brace for a Hashimoto’s symptom flare-up? Ahead, a look at the link between menstrual periods and autoimmune flare-ups.

An autoimmune Hashimoto's flare-up occurs when the immune system ramps up against what it perceives as a foreign invader. The immune system normally goes into action when it detects viruses, bacteria, or toxins. But with autoimmune disorders like Hashimoto’s, the immune system becomes dysregulated and causes an autoimmune reaction, attacking our own glands, tissues, and organs. As a result, other catalysts can overstimulate the immune response and trigger a flare-up, including physical or emotional stress, nutritional factors, and hormonal changes.

What are the symptoms of a Hashimoto’s flare-up?

When you have a Hashimoto’s flare-up, you may experience some of the more common symptoms, which include:

  • Fatigue
  • Insomnia
  • Muscle aches and joint pain 
  • Digestive issues
  • Brain fog
  • Headaches
  • Dizziness
  • Mental health changes
  • Puffiness

The relationship between menstrual cycles, autoimmunity, and flare-ups

We know that menstrual cycles and hormones can affect autoimmune diseases, including Hashimoto’s thyroiditis. In fact, autoimmune diseases are more likely to be diagnosed during periods of female hormone imbalance and significant hormonal change, such as puberty, after childbirth, and during perimenopause, and menopause.

Autoimmune symptom flare-ups – including flare-ups in Hashimoto’s disease symptoms – also appear to follow cycles that are tied to the hormonal changes that take place during the menstrual cycle, specifically:

  • The follicular phase: During the first part of the menstrual cycle, from the first day of a menstrual period until ovulation, increasing estrogen levels cause an immune response, with increasing antibodies and inflammation.
  • The luteal phase: The luteal phase –from ovulation until a few days before the start of the next menstrual period – is characterized by some degree of immune suppression and a reduction in inflammation.
  • Late luteal phase/menstruation: This phase, which runs from several days before the menstrual period until the start of the period, can be characterized by a worsening of autoimmune symptoms – a “flare-up” – along with an increase in inflammatory responses.

A BOOST Thyroid/University of Oxford study, co-authored by Paloma’s Dr. Vedrana Högqvist Tabor and published in the journal Trends in Ecology and Evolution, found that sex hormones affect the severity of a woman’s symptoms in many common autoimmune conditions, including Hashimoto’s disease, and that the symptoms – as well as female immunity – are cyclical. Specifically, at ovulation, the immune system is somewhat suppressed to prevent immune cells from potentially attacking a fertilized egg and interfering with pregnancy. This drop in the body’s immune defenses may allow for other immune activities – including attacks on the thyroid gland and flare-ups characteristic of Hashimoto’s – to increase during this time frame until after menstruation begins.

Hashimoto’s is not the only autoimmune disease that goes through these cycles. Other autoimmune conditions are known to go through flare-ups during the luteal or late luteal phase. For example, many women with multiple sclerosis (MS), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE) report worsening signs indicative of a flare-up in the days right before the start of a menstrual period.

While menstrual cycles may affect your Hashimoto’s symptoms, you should also be aware that the opposite is true. Hashimoto’s and hypothyroidism can affect your menstrual cycle. Specifically, Hashimoto’s and hypothyroidism can cause irregular periods or cycles when you don’t ovulate, contributing further to hormonal imbalances and the risk of cyclical flare-ups.

Will you have a Hashimoto’s flare-up around your period?

There’s no way to know in advance whether you will have a flare-up of Hashimoto’s symptoms around your menstrual period. Your experience is always the best predictor. You may have foreseeable and obvious Hashimoto’s flare-ups, while other women notice no difference or even experience a slight improvement in symptoms around their periods.

It can be challenging to determine whether your symptoms are related to your period or a Hashimoto’s flare-up because they are similar. The best way to determine the source of your symptoms is to carefully track both your menstrual period and your autoimmune symptoms and look for cyclical patterns or flare-ups in your thyroid symptoms. Knowledge is power! Map out your follicular and luteal phases, and know when to expect your period. That way, you can better correlate your autoimmune thyroid symptoms to your menstrual cycle and may be able to anticipate – and better prevent -- flare-ups before symptoms appear.

How can you control flare-ups?

While many of the risk factors and triggers for flare-ups – including the menstrual cycle -- are unavoidable, there are some things you can do to help control and minimize flare-ups.

First, ensure you get enough sleep because lack of sleep can impair healthy immune function and worsen Hashimoto’s flare-up symptoms around your menstrual period.

You should also pay attention to eating a nutrient-rich, healthy diet. Specifically, an anti-inflammatory diet before and during a flare-up may help shorten the length or reduce the intensity of symptoms. To help, you may want to follow Paloma’s Flare-Up Meal Plan.

You may also want to check out an article here at Paloma’s blog about other effective ways to manage an autoimmune flare-up.

Finally, some women have relief from autoimmune triggers with birth control pills or hormonal therapy to even out hormonal fluctuations. You can talk with your healthcare practitioner about whether this is an option.

See our Paloma Speaker Series video for more tips on how to get through a Hashimoto's flare-up. This video features Functional Nutritional Therapy Practitioner Shanna Nemrow and Holistic Health Coach Mckenzi Cohen, who share their advice about how to spot, avoid, and manage a Hashimoto's symptom flare-up.

A note from Paloma

Relief of Hashimoto’s and hypothyroidism symptoms, especially during menstrual flare-ups, starts with a foundation of optimal thyroid function and healthy levels of thyroid hormones. One way to stay on top of your thyroid hormone levels is periodic screening with the Paloma Complete Thyroid Blood Test kit. This easy, convenient, and affordable kit lets you test your thyroid from the comfort of your home. The Paloma home thyroid test kit includes all the supplies needed for sample collection and testing thyroid stimulating hormone (TSH), free T3, free T4, and Thyroid Peroxidase (TPO) antibody levels.

For thyroid diagnosis and treatment, you can schedule a virtual visit with one of our top thyroid doctors. Paloma’s thyroid practitioners work with you to prescribe thyroid medication that will safely normalize your thyroid function, help you balance your hormones, and relieve symptoms.


Alvergne A, Högqvist Tabor V. Is Female Health Cyclical? Evolutionary Perspectives on Menstruation. Trends in Ecology & Evolution. 2018;33(6):399-414. doi:10.1016/j.tree.2018.03.006

Oertelt-Prigione S. Immunology and the menstrual cycle. Autoimmunity reviews. 2012;11(6-7):A486-92. doi:10.1016/j.autrev.2011.11.023

Desai MK, Brinton RD. Autoimmune Disease in Women: Endocrine Transition and Risk Across the Lifespan. Frontiers in Endocrinology. 2019;10(265). doi:10.3389/fendo.2019.00265

Whitacre CC. Sex differences in autoimmune disease. Nature Immunology. 2001;2(9):777-780. doi:10.1038/ni0901-777

Whitacre CC. BIOMEDICINE: A Gender Gap in Autoimmunity. Science. 1999;283(5406):1277-1278. doi:10.1126/science.283.5406.1277

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Mary Shomon

Patient Advocate

Mary Shomon is an internationally-recognized writer, award-winning patient advocate, health coach, and activist, and the New York Times bestselling author of 15 books on health and wellness, including the Thyroid Diet Revolution and Living Well With Hypothyroidism. On social media, Mary empowers and informs a community of more than a quarter million patients who have thyroid and hormonal health challenges.

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