Lisa* thought she had her autoimmune symptoms under control—until perimenopause

For years, she managed her fatigue, joint pain, and brain fog with a solid routine. She avoided inflammatory foods, prioritized sleep, and followed her doctor’s treatment plan. But then, things began to change.

Some months, right before her period, it felt like her body was betraying her. Her fatigue became unbearable, her joints ached more than usual, and her brain fog made even simple tasks overwhelming.

She recalled that during pregnancy, something unexpected happened—she felt amazing. For the first time in years, her symptoms disappeared. But after giving birth, it was like a switch flipped. She was exhausted beyond belief, her hair started falling out, and her autoimmune symptoms came back with a vengeance.

As she approached perimenopause, Lisa noticed her flares became more frequent, her sleep quality worsened, and she felt like she was losing control of her body again.

Her doctors told her it would get better with time, was part of the menopause transition, and something she would need to learn to live with.

Why Hormones Matter in Autoimmune Disease

Lisa isn’t alone—autoimmune diseases disproportionately affect women, and hormones play a major role.

​New research from Stanford suggests this may be related to women having two X chromosomes. The researchers aptly note that half the population lives without a Y chromosome, but every human needs at least one X chromosome. In people with two X chromosomes, this can lead to double trouble. Why? Because one of these chromosomes must be turned “off” early in fetal development, when it is reactivated in any capacity, harm may occur. The silenced chromosome may be influenced by the environment, infections, hormones, and other triggers. When this happens, it creates dysfunctional cell signals that impact the immune system and how it interacts with the female sex hormones estrogen and progesterone.

While there is more research to understand, key attributes about the female sex hormones' impact on autoimmunity include:

🔹 Estrogen is a double-edged sword – At normal levels, it can have a protective effect against inflammation, but when it fluctuates (like before a period or during menopause), it can “confuse” the immune system.
🔹 Progesterone helps regulate the immune system – When progesterone drops (like after pregnancy), autoimmune symptoms can flare.
🔹 Hormonal shifts can trigger autoimmune disease – Many women develop autoimmune conditions for the first time during puberty, pregnancy, postpartum, or perimenopause—major life stages tied to hormonal changes.
🔹 Postpartum flares are real – Some women experience remission during pregnancy (thanks to high progesterone), only to have a severe autoimmune flare in the months following childbirth. This may be when the disease first presents as well, and an initial diagnosis of an autoimmune disease is made.
🔹 Perimenopause and menopause create new challenges – Declining estrogen and progesterone levels can lead to increased inflammation, worsening joint pain, brain fog, and fatigue.

For women with autoimmune diseases, hormones can mean the difference between feeling great and feeling awful.

How to Regain Control

If your symptoms seem to follow a hormonal pattern, it’s time to take action.

Track Your Symptoms

Start keeping a symptom journal to identify patterns. Do your symptoms flare at specific points in your cycle? Did things change after pregnancy or when you started birth control? This data can help guide better treatment.

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Naturally Support Your Hormone Health

Several lifestyle choices you make daily can worsen hormone fluctuations and autoimmune flares. Things you can try:
✅ Eat plant-based or lean protein with every meal
✅ Eat nuts and seeds, leafy greens, cruciferous vegetables, and berries to reduce inflammation
✅ Avoid processed carbs and artificial or natural sugars; keep fruit and grain servings small
✅ Walk for 10-15 minutes after meals to help lower blood glucose and insulin levels
✅ Prioritize better sleep quality to decrease insulin resistance and support hormone balance
✅ Manage stress to keep cortisol levels in check

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Work with a Physician Who Understands Both Autoimmune and Hormonal Health

Not all healthcare professionals are experts in all areas, and many are looking through a specialty rather than a generalist lens. This is why many will not connect the dots between hormones and autoimmunity. If your symptoms seem to fluctuate with your cycle, pregnancy, or menopause, you need someone who will take your concerns seriously, but also someone who sees the “big picture”.

Consider Advanced Testing

If you suspect hormone imbalances are fueling your autoimmune flares, testing can provide answers. Consider:
🩸 Comprehensive panels – Look at liver, kidney, bone marrow, thyroid, and immune levels
🩸 Inflammatory markers – CRP, ESR, and other markers can reveal underlying inflammation.

Your Symptoms Are Not “In Your Head”

Lisa spent years thinking her flares were random—until she understood the hormone-autoimmune connection. Once she started tracking her symptoms and supporting her body, she finally regained control.

If you’ve been told “it’s only your hormones” or that your symptoms are unrelated to your cycle, pregnancy, or menopause, it’s time to dig deeper.

🔹 Share this email to help other women struggling with unexplained flares. Because when you understand the hormone-autoimmune connection, you can finally take back control. 💙

To Your Health,

Amy Loden Tiffany, MD

*Name changed to protect privacy.

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