Can menopause trigger a new autoimmune disease?

Midlife often is marked by experiencing several of the extensive possibilities of physical changes and symptoms, including fatigue, joint aches, mood swings, and brain fog. Women chalk these symptoms up to menopause (because what else could it be?), however, in some cases, these symptoms may be due to another condition that needs addressed. 

 “Some women are asymptomatic (no symptoms), and may still have an autoimmune condition without even knowing it. Some conditions may be discovered incidentally. Women who seek care during the vulnerable period of time of “transition” and early menopause can benefit. Taking the time to “reframe” your health needs and optimize your health may uncover conditions that, when addressed, will further impact your health positively and your well-being." ~ Dr. Stephanie Culver

How Menopause Affects the Immune System

Estrogen levels begin to decline during perimenopause, before eventually reaching their lowest point in menopause. While estrogen is closely linked to reproductive health, it’s also instrumental in regulating immune function. As your levels shift during perimenopause, your immune system starts responding differently, sometimes becoming more prone to inflammation or immune dysregulation.

Estrogen helps regulate how immune cells respond to threats in your body. It can calm certain inflammatory pathways while supporting your ability to fend off infection. As estrogen levels fall during menopause, that steady regulatory effect begins to change.

Research suggests that perimenopause and elevated inflammation levels are linked. Changes in hormone levels can affect immune cell behavior, inflammatory signaling, and even gene expression through epigenetic pathways. As estrogen levels decline, that regulatory effect weakens, which can allow inflammatory pathways to become more active and, in some cases, increase the likelihood of immune misfires (like the immune system accidentally targeting healthy tissue).

For some women, this may increase the likelihood of developing an autoimmune disease or alter the course of an existing one in midlife. Because many autoimmune symptoms overlap with menopause symptoms, recognizing what’s “normal” and what may deserve a closer look is key.

Can Menopause Trigger New Autoimmune Diseases?

Data show that 67% of autoimmune disease diagnoses in the United States are in women. Hormonal changes are thought to play a role in their development.

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While menopause doesn’t directly cause autoimmune diseases, research suggests that the hormonal transition may influence when or how these conditions appear. For some women, menopause may coincide with the onset of a new autoimmune condition. For others, it may change the course of an existing one, sometimes improving symptoms, and other times worsening them.

Some of the strongest evidence that shows estrogen’s impact on autoimmunity exists for the autoimmune rheumatic conditions, such as  Rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). Research in this area is ongoing. 

Keep in mind that although autoimmune diseases present themselves more often in midlife women than men, not all menopausal women will develop an autoimmune disease.  Similarly, that doesn’t mean that women with existing conditions will experience more intense menopausal symptoms. Your risk depends on your genetic factors, environmental exposures, and unique health history.

Which Autoimmune Diseases Are Linked to Menopause?

Researchers have looked at how menopause affects several autoimmune conditions, but rheumatoid arthritis (RA) is by far the most well-studied. Some studies point to women with RA having more intense symptoms or changes in how the disease shows up during transition and into menopause.

In addition, the relationship between SLE and menopause appears to be bidirectional, meaning each can affect and impact the other. It’s true: Women who enter menopause earlier may have a higher likelihood of developing SLE (and RA) compared to those who reach menopause later. At the same time, women living with SLE may be more susceptible to entering menopause earlier in life. This can occur either due to the condition itself or the medications used to manage it.

Newer studies are also investigating the possible links between menopause-related immune changes and conditions like autoimmune thyroid disease (namely Hashimoto’s thyroiditis), multiple sclerosis, and Sjögren’s syndrome.

Recognizing Symptoms: Menopause vs. Autoimmune Disease

We can’t emphasize this message enough: The symptoms that you’re feeling are not in your head! But trying to figure out which symptoms are coming from what can be confusing, especially given how much overlap there is between menopause and certain autoimmune diseases. 

Think about it, some of the most common menopause symptoms, including fatigue, joint pain, sleep disruption, and mood changes, are also symptoms of autoimmune diseases like rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE). Autoimmune diseases may also show up with a host of other issues, including rashes, muscle weakness, dry eyes, and even recurring low-grade fevers.

As if that weren’t enough to manage, musculoskeletal pain can also become more apparent during menopause. While it’s true that joint stiffness or soreness can be related to hormonal changes, as well as overuse, assuming your new pain is menopause-related may not be accurate. Think of yourself as your own personal detective, tracking symptom patterns to help identify when and where they show up.

When Should You See a Healthcare Provider?

“Because we know autoimmune conditions impact women more often than men, and present more often in midlife, I recommend that at annual visits to discuss the addition of laboratories along with the standard comprehensive labs. Constitutional symptoms such as fatigue, depression, and malaise should be taken seriously and not attributed to “aging” and “”stress”. These vague and common complaints can represent the signs of an autoimmune condition.”  - Dr. Stephanie Culver

When women are in perimenopause and experiencing hormonal changes, this can further impact and shake things up. Important to note, that not every symptom should be written off as “just hormones.” If you’re experiencing unusual symptoms such as unexplained joint swelling, new skin rashes, or debilitating fatigue that doesn’t get better with rest (no matter how many hours of sleep you get), it’s probably worth checking in with a healthcare provider. 

Identifying autoimmune diseases early can improve your health long-term and help you manage your symptoms more effectively.  A menopause-trained clinician can help distinguish between symptoms related to hormonal changes and those that may signal an underlying autoimmune condition. Frequently, both effective management directed at the autoimmune condition and also caring for menopause symptoms delivers optimized relief and better health overall. 

MHT for Autoimmune Disease and Menopause

If you’re navigating an autoimmune condition during menopause, it’s worth having a conversation with your doctor about options that support both your immune system and your hormonal health. Treatment often includes a combination of therapeutic approaches, such as medications to manage the autoimmune condition as well as focusing on lifestyle changes that can lower inflammation and ease symptoms.

Menopause hormone therapy (MHT) is just one option that may help. While MHT may be restricted in it’s use for some women or not a desired treatment, some research suggests it may improve both menopause symptoms and certain autoimmune-related symptoms. A menopause-informed clinician can help you weigh the benefits and risks and figure out whether hormone therapy makes sense and would likely have a positive impact alongside other medications you may be taking.

Empowering Yourself: Monitoring, Prevention, and Self-Advocacy

Whether or not you have a known autoimmune condition, menopause itself calls for proactive health monitoring and optimization.  Keeping up with your annual exams, regular doctor check-ups, tracking new or changing symptoms, eating a nutrient-dense diet, engaging in physical activity, managing stress levels, and prioritizing restorative sleep will can help alleviate symptoms and feel more comfortable day-to-day.

While lifestyle habits alone can’t prevent autoimmune disease, the above lifestyle habits can support your immune system and emotional well-being.

By now, you probably noticed that menopause can impact your body in many ways, including your immune system. Autoimmune conditions can introduce  new challenges and unfamiliar symptoms. Remember, you know your body best; trust your insight. If something you experience feels off or different, it’s okay to ask questions or seek a second opinion. You deserve validation of your individualized health history.

Frequently Asked Questions

Can menopause actually cause an autoimmune disease?

While menopause does not directly cause autoimmune diseases, the hormonal transition—specifically the decline in estrogen—can influence when and how these conditions appear. Estrogen plays a vital role in regulating the immune system and calming inflammatory pathways. As levels drop during perimenopause and menopause, the immune system may respond differently, potentially leading to immune "misfires" or the onset of conditions like rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) in genetically predisposed individuals.

How can I tell the difference between menopause symptoms and an autoimmune condition?

Distinguishing between the two is challenging because many symptoms overlap, including fatigue, joint aches, mood swings, and brain fog. However, certain "red flag" symptoms may suggest an autoimmune issue rather than just hormonal changes. These include unexplained joint swelling, new skin rashes, muscle weakness, dry eyes, or recurring low-grade fevers. Tracking your symptom patterns and discussing them with a menopause-trained clinician can help determine if the issues are hormonal or require more comprehensive laboratory testing.

Does menopause hormone therapy help with autoimmune symptoms?

Menopause hormone therapy (MHT) is an option that may support both hormonal health and the immune system. Some research suggests that MHT can improve menopause symptoms while also positively impacting certain autoimmune-related symptoms by stabilizing hormone levels. Because every health history is unique, it is important to consult with a healthcare provider to weigh the risks and benefits of MHT, especially if you are already taking medications to manage a diagnosed autoimmune condition.