What are the criteria for granting a medical exemption from COVID-19 vaccination for patients with autoimmune disorders?

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Last updated: October 15, 2025View editorial policy

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Medical Exemption for COVID-19 Vaccination in Patients with Autoimmune Disorders

COVID-19 vaccination is generally recommended for patients with autoimmune disorders, with only rare specific circumstances warranting a medical exemption. 1

Criteria for Medical Exemption

  • Medical exemptions for COVID-19 vaccination in autoimmune disorder patients should be limited to:

    • Patients with documented severe allergic reaction (anaphylaxis) to a previous dose of COVID-19 vaccine or known allergy to vaccine components such as polyethylene glycol (PEG) in mRNA vaccines or polysorbate in adenoviral vector vaccines 1

    • Patients with life-threatening autoimmune disease flares requiring ICU-level care, where vaccination should be temporarily deferred until the condition is better controlled 1

    • Patients who experienced a documented severe adverse reaction to the first dose of a COVID-19 vaccine that contraindicates receiving subsequent doses 1

General Vaccination Recommendations for Autoimmune Patients

  • The American College of Rheumatology strongly recommends that patients with rheumatic and musculoskeletal diseases (RMDs) including autoimmune inflammatory rheumatic diseases (AIIRDs) receive COVID-19 vaccination 1

  • Vaccination should occur as soon as possible for autoimmune patients, irrespective of disease activity and severity, except in cases of immediately life-threatening disease 1

  • There is no preference for one COVID-19 vaccine over another for autoimmune patients; they should receive whichever authorized vaccine is available to them 1

Medication Timing Considerations

  • Most immunomodulatory therapies can be continued without modification during vaccination 1

  • For specific medications that may reduce vaccine efficacy, timing adjustments may be considered:

    • Methotrexate: Consider withholding for 1 week after each vaccine dose in patients with well-controlled disease 1

    • Rituximab: If disease activity allows, delay rituximab 2-4 weeks after the second vaccine dose or schedule vaccination at least 4-6 months after the last rituximab dose 1

    • JAK inhibitors: Consider withholding for 1 week after each vaccine dose 1

    • Abatacept: For subcutaneous form, withhold 1 week before and after first dose; for IV form, time vaccination 4 weeks after infusion 1

Risks and Benefits

  • The risk of COVID-19 infection and complications in autoimmune patients outweighs the theoretical risk of vaccine-induced disease flares 1, 2

  • While there have been case reports of new-onset autoimmune conditions or flares following COVID-19 vaccination, these are rare compared to the clear mortality and morbidity benefits of vaccination 3, 4

  • Some studies suggest COVID-19 vaccination may trigger autoimmune diseases in predisposed individuals, but the causal relationship remains to be definitively established 5

  • Patients with autoimmune disorders are at increased risk of severe COVID-19 outcomes, making vaccination particularly important for this population 1, 6

Sample Medical Exemption Letter Format (for rare qualifying cases only)

[Date]
[Healthcare Provider Name and Credentials]
[Medical Practice Name]
[Address]
[Phone/Email]

RE: Medical Exemption from COVID-19 Vaccination

To Whom It May Concern:

This letter certifies that [Patient Name], DOB [Date of Birth], has been evaluated and has [specific qualifying medical contraindication] that meets the criteria for medical exemption from COVID-19 vaccination according to current medical guidelines.

This contraindication is [permanent/temporary until (date)].

This exemption is based on [specific evidence-based reason, e.g., "documented severe allergic reaction to polyethylene glycol, a component of mRNA COVID-19 vaccines" or "currently experiencing life-threatening autoimmune disease flare requiring intensive care management"].

Alternative COVID-19 prevention measures are recommended for this patient, including [specific recommendations].

This patient should be re-evaluated for vaccination eligibility on [date] if this is a temporary exemption.

Sincerely,
[Physician's Signature]
[Physician's Name, Credentials]
[License Number]

Important Caveats

  • Medical exemptions should be rare and based on specific contraindications, not general diagnosis of an autoimmune condition 1

  • Patients granted temporary exemptions should be reassessed regularly as their clinical situation changes 1

  • Patients with autoimmune disorders who receive exemptions should be counseled on alternative protective measures including masking, physical distancing, and ensuring household contacts are vaccinated 1

  • Healthcare providers should document the specific contraindication and rationale for exemption in detail 1

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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