Is It Hormones—or Is It Autoimmunity? Maybe It's Both

Many women with autoimmune conditions notice that their symptoms shift throughout the month—particularly around their periods or ovulation. These symptom flares may reflect deeper interactions between hormones and the immune system. Oestrogen and progesterone are not just reproductive hormones—they’re powerful immune modulators.

How the Menstrual Cycle Shapes Immune Activity

The menstrual cycle is far more than a reproductive rhythm—it’s a shifting hormonal landscape that interacts intimately with the immune system.

• Follicular Phase (Days 1–13): Oestrogen rises as the uterine lining regenerates. This increase recruits more immune cells—particularly macrophages—into reproductive tissues.

• Ovulation (Around Day 14): Oestrogen peaks, triggering an LH surge. For some women, this can heighten immune activation, resulting in flares. 

• Luteal Phase (Days 15–28): Progesterone becomes dominant, exerting calming, immunosuppressive effects.

• Menses (Day 1 of a New Cycle): A sharp drop in both oestrogen and progesterone can provoke autoimmune flares.

  
  

Hormones as Immune Regulators

• Oestrogen can either suppress or stimulate the immune system depending on levels and timing. It increases IL-4 and decreases NF-κB, yet excessive levels may ramp up antibody production and autoimmune activity.

• Progesterone fosters immune tolerance by promoting regulatory T cells (Tregs) and modulating inflammatory cytokines.

• LH also influences Tregs, further linking reproductive and immune systems.

  
  

These hormonal shifts explain why some women feel well at certain times of the month but symptomatic at others—often delaying diagnosis or masking chronic immune dysfunction.

Hormonal Imbalance: When Oestrogen Outpaces Progesterone

When oestrogen levels rise unopposed—due to anovulatory cycles, poor detoxification, or xenoestrogen exposure—immune tolerance can break down.

Causes of Oestrogen Dominance:

• Anovulatory cycles (common in adolescence, PCOS, perimenopause, or hypothyroidism)

• Xenoestrogens (e.g., BPA, phthalates, parabens)

• Obesity (adipose tissue increases oestrogen and inflammatory cytokines)

• Impaired detoxification (poor liver function, sluggish digestion)

  
  

Why Progesterone Matters:

Progesterone is only produced after ovulation. It has broad physiological benefits that directly support autoimmune resilience:

• Promotes immune tolerance and counters oestrogen

• Enhances stress regulation and thyroid sensitivity

• Supports sleep, cardiovascular health, and bone density

• Helps maintain lean muscle and metabolic balance

Clinical signs of luteal phase insufficiency may include a short luteal phase, low post-ovulation temperatures, persistent cervical mucus, and premenstrual spotting.

Hormonal Contraceptives and Immune Disruption

Hormonal contraceptives prevent pregnancy by suppressing ovulation—but in doing so, they may disrupt the beneficial immune effects of natural oestrogen and progesterone.

What the Research Says:

• Combined oral contraceptives have been linked to increased risk of lupus, Crohn’s, MS, and interstitial cystitis

• Synthetic progestins may bind multiple receptors (not just progesterone), with downstream effects on mood, immune regulation, and stress response

• Contraceptives may raise C-reactive protein, a marker of inflammation

  
  

Not every woman will respond negatively—but for those with autoimmune risk, hormonal contraceptives can be a tipping point.

Conclusion: Listening to the Cycle

For many women with autoimmune conditions, symptom flares aren’t random — they’re rhythmic. Hormonal fluctuations throughout the menstrual cycle can act as both a trigger and a clue, revealing important insights into immune health. Oestrogen and progesterone do more than govern reproduction; they shape immune tolerance, inflammatory responses, and vulnerability to flare-ups.

Recognising these patterns matters. If symptoms worsen around ovulation or before menstruation, it may not be “just hormones” — it could be a signal that immune balance is being disrupted.

Autoimmunity is complex, but understanding how hormones interact with the immune system opens up new possibilities — not just for symptom relief, but for building resilience month by month. Your cycle holds valuable information and it’s time we started listening.