Vaccines and Autoimmune Disease: What You Need to Know Before Your Next Shot

Why vaccination matters more, not less, with autoimmune disease

People with autoimmune conditions often face a higher risk of serious infections — both because of the underlying disease and because many of the medications used to treat it suppress immune function. Infections that are mild in healthy adults can be severe or life-threatening in someone on immunosuppressive therapy.

This is why major organizations including the ACIP, the American College of Rheumatology, and subspecialty societies consistently recommend staying up to date on vaccinations rather than avoiding them 1Ref 1Wodi AP, Issa AN, Moser CA, Cineas S (2025).Advisory Committee on Immunization Practices Recommended Immunization Schedule for Adults Aged 19 Years or Older — United States, 2025.Live vs. inactivated vaccine classification; recommendations for immunocompromised adults; flu, hepatitis B, and COVID-19 recommendations; timing relative to immunosuppressive therapy. The risk of skipping a vaccine is, in most cases, higher than the risk of receiving it.

The core distinction: inactivated vs. live vaccines

Inactivated vaccines contain killed virus or bacteria, or just a protein piece of the pathogen. They cannot cause infection. Examples include:

• Influenza (injected flu shot)
• COVID-19 mRNA vaccines
• Tdap and Td
• Hepatitis A and hepatitis B
• HPV
• Pneumococcal vaccines (PCV15, PCV20, PPSV23)
• Recombinant shingles vaccine (Shingrix)

These are generally safe for people with autoimmune diseases, including those on immunosuppressive medications 1Ref 1Wodi AP, Issa AN, Moser CA, Cineas S (2025).Advisory Committee on Immunization Practices Recommended Immunization Schedule for Adults Aged 19 Years or Older — United States, 2025.Live vs. inactivated vaccine classification; recommendations for immunocompromised adults; flu, hepatitis B, and COVID-19 recommendations; timing relative to immunosuppressive therapy.

Live attenuated vaccines contain a weakened, living version of a pathogen. Because the organism can replicate to a limited degree, there is a theoretical risk that someone with a severely suppressed immune system could develop a vaccine-strain infection. Live vaccines include:

• MMR (measles-mumps-rubella)
• Varicella (chickenpox)
• LAIV (nasal flu spray)
• Yellow fever
• Zostavax (the older shingles vaccine, now largely replaced by Shingrix)

These require careful evaluation before being given to anyone who is significantly immunosuppressed.

How your medications change the picture

Many people with autoimmune diseases take medications that suppress the immune system: biologics (TNF inhibitors, IL-6 blockers, B-cell depleting agents like rituximab), DMARDs such as methotrexate, high-dose corticosteroids, or JAK inhibitors.

These medications affect vaccine safety and effectiveness in different ways:

Safety: Some drugs — especially B-cell depleting agents and certain biologics — make live vaccines contraindicated while you are taking them. The risk of vaccine-strain illness is too high.

Effectiveness: Immunosuppressants can reduce how well your immune system responds to a vaccine, meaning it may provide less protection than it would off medication. Some specialists recommend timing vaccines before starting a new immunosuppressant, or during a medication window if medically feasible.

This timing decision belongs to your rheumatologist, neurologist, or gastroenterologist — whoever manages your condition — in collaboration with your primary care clinician 1Ref 1Wodi AP, Issa AN, Moser CA, Cineas S (2025).Advisory Committee on Immunization Practices Recommended Immunization Schedule for Adults Aged 19 Years or Older — United States, 2025.Live vs. inactivated vaccine classification; recommendations for immunocompromised adults; flu, hepatitis B, and COVID-19 recommendations; timing relative to immunosuppressive therapy.

Which vaccines are especially important with autoimmune disease?

Influenza (flu): Annual inactivated flu vaccine is recommended. People on immunosuppressants are at particular risk for severe flu complications 1Ref 1Wodi AP, Issa AN, Moser CA, Cineas S (2025).Advisory Committee on Immunization Practices Recommended Immunization Schedule for Adults Aged 19 Years or Older — United States, 2025.Live vs. inactivated vaccine classification; recommendations for immunocompromised adults; flu, hepatitis B, and COVID-19 recommendations; timing relative to immunosuppressive therapy.

Pneumococcal: Recommended at earlier ages than the general population for many autoimmune conditions. Current ACIP guidance supports PCV20 or a PCV15/PPSV23 sequence for adults with immunocompromising conditions 2Ref 2Kobayashi M, Pilishvili T, Farrar JL, et al. (2023).Pneumococcal Vaccine for Adults Aged ≥19 Years: Recommendations of the Advisory Committee on Immunization Practices, United States, 2023.Pneumococcal vaccine recommended at earlier ages and with broader indications for immunocompromising conditions.

Shingles (Shingrix): People on immunosuppressive therapy are at elevated risk for shingles and post-herpetic neuralgia. Shingrix is a recombinant (non-live) vaccine, so it can be given to most immunosuppressed patients — this is one of the most clinically significant recent changes in vaccine guidance for this population 3Ref 3Dooling KL, Guo A, Patel M, et al. (2018).Recommendations of the Advisory Committee on Immunization Practices for Use of Herpes Zoster Vaccines.Shingrix (recombinant, non-live) recommended for immunosuppressed patients; elevated shingles risk in immunocompromised populations.

COVID-19: Recommended; people who are immunocompromised may need additional primary doses or more frequent boosters. Discuss current guidance with your clinician.

Hepatitis B: Recommended for many patients on biologics, who are at elevated risk of hepatitis B reactivation and complications.

What to do before your next vaccine

Before any vaccination, bring up your autoimmune condition and your complete medication list — drug name, dose, and duration. If you see both a specialist and a primary care provider, ask one to coordinate with the other or explicitly confirm that both are in the loop.

Do not skip vaccines out of unspecified fear without having that conversation. If there is uncertainty about a live vaccine, ask whether an inactivated alternative exists:

• Shingrix instead of Zostavax for shingles
• Injected flu shot instead of nasal spray
• Inactivated polio vaccine (IPV) instead of oral (no longer used in the U.S., but relevant for travel)

If you are about to start a new immunosuppressant, ask your prescribing clinician whether there is a window to complete any outstanding live vaccines beforehand 1Ref 1Wodi AP, Issa AN, Moser CA, Cineas S (2025).Advisory Committee on Immunization Practices Recommended Immunization Schedule for Adults Aged 19 Years or Older — United States, 2025.Live vs. inactivated vaccine classification; recommendations for immunocompromised adults; flu, hepatitis B, and COVID-19 recommendations; timing relative to immunosuppressive therapy.