What causes autoimmune symptoms? A clear explanation for patients

By Sina Hartung, MMSC-BMI, Harvard Medical SchoolReviewed by Eureka Health Medical Group
Published: July 9, 2025Updated: July 9, 2025

Summary

Autoimmune symptoms happen when our immune system mistakes healthy tissue for a threat. This misfire is driven by a mix of inherited genes, past infections, hormone shifts, gut-microbiome imbalance, certain drugs and environmental triggers like smoking or silica dust. The result is a chronic, self-sustaining cycle of inflammation that produces joint pain, rashes, brain fog, fatigue and many other complaints.

Why does the immune system attack healthy tissue in autoimmune disease?

Autoimmunity starts when immune cells lose tolerance to the body’s own proteins. Genetic risk primes the system; infections or toxins flip the switch. Once self-proteins are targeted, inflammation becomes chronic and symptoms appear.

  • Genes load the gunMore than 100 gene variants—especially HLA-DR and PTPN22—raise autoimmune risk; identical-twin studies show up to 50 % concordance for type 1 diabetes.
  • Infections pull the triggerViruses like Epstein–Barr can mimic self-proteins (molecular mimicry), prompting B cells to make cross-reactive antibodies.
  • Hormones add fuelEstrogen boosts antibody production, explaining why 78 % of autoimmune patients are women.
  • Leaky gut opens the doorA damaged intestinal lining lets bacterial fragments slip into blood, activating systemic immunity.
  • Quote from Sina Hartung, MMSC-BMI"Think of autoimmunity as a perfect storm—genes create the conditions, but environment decides when lightning strikes."
  • Pollutants amplify genetic riskNIEHS research shows that exposures to pesticides, organic mercury, and cigarette smoke can interact with susceptibility genes and heighten the chance of developing autoimmune disorders such as rheumatoid arthritis. (NIEHS)
  • Autoimmunity affects 23.5 million AmericansJohns Hopkins Medicine estimates at least 23.5 million U.S. residents live with an autoimmune disease and nearly 80 % of those affected are women. (JHM)

References

Which autoimmune symptoms should make me seek care right away?

Most autoimmune flares are uncomfortable but not dangerous. Certain warning signs, however, can signal organ-threatening inflammation that needs urgent evaluation.

  • Sudden shortness of breathCould mean lupus pneumonitis or pulmonary embolism in antiphospholipid syndrome—call 911.
  • New neurologic deficitsNumbness, double vision, or foot-drop may herald multiple sclerosis relapse that benefits from high-dose steroids within 48 hours.
  • Rapidly enlarging purple rashVasculitis can compromise blood flow; skin biopsy and immunosuppressants are often needed.
  • Persisting fever above 101 °F for three daysMay signal hemophagocytic syndrome in systemic juvenile arthritis, a medical emergency.
  • Quote from the team at Eureka Health"Autoimmune red flags often look like infections; if you are not sure, assume the worst and contact a clinician immediately."
  • Unexpected bleeding or easy bruisingGoodRx lists “signs of bleeding” such as blood in stool, vomiting blood, or new bruises as red-flag autoimmune symptoms that need immediate medical attention. (GoodRx)
  • Resting heart rate above 100 beats per minuteEurekaHealth advises seeking urgent care if a Hashimoto’s flare raises your resting pulse over 100 bpm, as this can signal life-threatening thyroid storm or severe inflammation. (EurekaHealth)

References

How do genetics, infections, and hormones interact to trigger flares?

Flares happen when several risk factors converge. Understanding the interplay can help predict and even prevent episodes.

  • Viral reactivation plus estrogen surge equals lupus flareStudies show anti-EBV antibodies triple during the week before many systemic lupus erythematosus (SLE) flares.
  • Stress hormones shift the immune set-pointElevated cortisol initially dampens immunity, but rebound cytokine release can follow, worsening rheumatoid arthritis pain 48 hours later.
  • Seasonal vitamin D drops unmask MS lesionsRelapse rates rise 14 % each winter when 25-OH-D falls below 30 ng/mL.
  • Gut dysbiosis tilts T-cell balanceLow Firmicutes and high Bacteroidetes ratios correlate with higher interleukin-17, a key driver of psoriasis plaques.
  • Quote from Sina Hartung, MMSC-BMI"You rarely get a flare from a single hit; it’s the cumulative burden of triggers that tips the scale."
  • Women carry 80 % of autoimmune diagnosesRoughly four out of five autoimmune patients are female, suggesting estrogen signaling and X-chromosome gene dosage augment genetic susceptibility and heighten flare risk. (GAI)
  • Environment shapes 77 % of immune variabilityA Stanford twin analysis showed that lifestyle and environmental exposures account for 77 % of differences in immune system activity, illustrating how infections or hormone fluctuations can overpower shared genetics and precipitate flares. (WillCole)

References

What daily habits can calm an overactive immune system?

Lifestyle adjustments cannot cure autoimmunity, but they can reduce flare frequency and intensity by lowering baseline inflammation.

  • Prioritize 7–8 hours of sleepShort sleep raises C-reactive protein by up to 25 % the next morning.
  • Adopt a Mediterranean-style dietHigh omega-3 intake lowers rheumatoid arthritis pain scores by 20 % in three months.
  • Quit smoking completelySmoking doubles risk of rheumatoid nodules and blunts biologic drug response.
  • Practice paced breathing or yogaTen minutes daily lowers interleukin-6 levels within six weeks, easing fatigue.
  • Quote from the team at Eureka Health"Small, consistent habits compound; our patients who track sleep and diet in the app report 30 % fewer flares."
  • Daily stress-management practices cut flare riskUp to 80 % of people with autoimmune disease recall a significant emotional stressor before onset; incorporating meditation or mindfulness can buffer cortisol spikes and lower inflammatory cascades that trigger flare-ups. (AI)
  • Replace ultra-processed snacks with antioxidant-rich whole foodsKaiser Permanente notes that fiber-filled grains, legumes, berries, leafy greens and unsaturated fats help quiet chronic inflammation, whereas refined sugars and processed foods do the opposite—so swapping the latter for the former supports steadier immune regulation. (Kaiser)

References

Which lab tests and treatments are most useful for unexplained autoimmune symptoms?

Targeted testing guides therapy. Empiric steroids help some patients, but the goal is precise treatment based on objective data.

  • Antinuclear antibody (ANA) test has high sensitivityA negative ANA makes systemic lupus unlikely (95 % negative predictive value).
  • C-reactive protein (CRP) tracks inflammation in real timeA CRP jump of more than 10 mg/L often precedes clinical flare by 24–48 hours.
  • DMARDs modify disease, not just symptomsMethotrexate reduces joint-erosion progression by 70 % in rheumatoid arthritis at two years; discuss risks with your rheumatologist.
  • Biologic drugs target single cytokinesAgents blocking TNF-α or IL-17 cut psoriasis surface area by 75 % in many trials but increase infection risk.
  • Quote from Sina Hartung, MMSC-BMI"Lab trends tell us when to act; medications then have a clear target, reducing trial-and-error prescribing."
  • Disease-specific antibody panels confirm diagnoses after a positive ANAOnce an ANA screen is positive, ordering targets such as anti-dsDNA, anti-Smith, RF, or anti-CCP narrows the differential and guides selection of immunosuppressive drugs. (Testing.com)
  • Bundled lupus panels aid earlier detection in high-risk familiesPatients with a strong family history benefit from comprehensive panels—ANA plus anti-dsDNA, complements, and urinalysis—that can reveal subtle disease activity before obvious symptoms emerge. (RupaHealth)

References

How can Eureka's AI doctor pinpoint my autoimmune triggers?

Eureka’s AI collects symptom logs, wearable data, and prior labs to spot patterns humans miss. It flags possible triggers and suggests next steps that a clinician can review.

  • Daily symptom correlationThe algorithm matches fatigue spikes with sleep debt or diet changes within a 24-hour window.
  • Automated flare forecastingCRP and heart-rate variability trends allow a 70 % accurate two-day flare prediction for many users.
  • Personalized lab recommendationsIf hair loss clusters with joint pain, Eureka may suggest thyroid antibody testing and routes the request to a physician for approval.
  • Quote from the team at Eureka Health"Our goal is not to replace your rheumatologist but to give you data they can act on."

Why do users with autoimmune concerns keep Eureka's AI doctor on their phone?

People living with chronic illness need continuous support. Eureka offers private, on-demand guidance without judgment.

  • 24/7 triage reduces clinic visitsUsers report 40 % fewer unnecessary urgent-care trips after six months.
  • Medication adherence remindersTimely alerts cut missed doses of DMARDs by 32 %, improving disease control.
  • High user satisfactionIndividuals tracking autoimmune symptoms rate the app 4.7 out of 5 stars for usability and trust.
  • Free and secureData are encrypted end-to-end; only you and your care team can access your information.
  • Quote from Sina Hartung, MMSC-BMI"For many, Eureka feels like having a knowledgeable friend who never forgets the details."

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Frequently Asked Questions

Can stress alone cause an autoimmune disease?

Stress does not create autoimmunity by itself, but chronic stress can tip the immune system into a flare if you already carry genetic risk.

Are autoimmune diseases contagious?

No. They result from your own immune system, not from an infection you can pass to others.

Which foods should I avoid during a flare?

Evidence suggests cutting added sugars, highly processed snacks and excess alcohol, all of which raise inflammatory markers.

Is it safe to get vaccines if I have lupus?

Most inactivated vaccines are safe and recommended; live vaccines may be deferred if you take strong immunosuppressants—ask your doctor.

Can probiotics help autoimmune symptoms?

Certain strains (for example, Lactobacillus rhamnosus GG) modestly lower CRP, but benefits vary and do not replace medical therapy.

How long before a new DMARD shows effect?

Traditional DMARDs like methotrexate may take 6–12 weeks before joint pain improves; steroids can bridge that gap if prescribed.

Does pregnancy worsen autoimmune disease?

Some diseases like rheumatoid arthritis often improve during pregnancy, while others like lupus may flare; close monitoring is essential.

What reference range of vitamin D is best for autoimmune patients?

Many specialists aim for serum 25-OH-D between 40 and 60 ng/mL, but targets should be individualized.

Can I ever stop taking my biologic if I feel better?

Stopping suddenly can lead to rebound inflammation; taper only under a rheumatologist’s guidance.

This content is for informational purposes only and is not intended as medical advice. Always consult with a qualified healthcare provider for diagnosis, treatment, and personalized medical recommendations.

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