White puzzle pieces interconnected with one piece labeled "vaccine"

COVID Vaccine & Autoimmune Disease FAQ

Over the course of the pandemic, Global Autoimmune Institute has stayed abreast of research on the novel coronavirus and its impact on those living with autoimmune disease. As public health measures around COVID-19 vaccines continue to evolve, we have received an influx of questions from the autoimmune disease community. While we are unable to provide medical advice or guidance about individual health plans, we would like to share answers to our most frequently asked questions!

  1.  Which vaccine should I get?
  2.  Is it safe for me to get the COVID-19 vaccine?
  3.  Will the vaccine work for me?
  4.  How will my autoimmune disease medications interact with the vaccine?
  5.  Am I at risk of experiencing a flare-up from the vaccine?
  6.  I was vaccinated and have experienced side effects – what should I do now?
  7.  Where can I find clinical trial data on people with autoimmune diseases getting the COVID-19 vaccine?
  8.  Should I get both doses of the vaccine if I’ve previously been infected with COVID-19?
  9.  Should I get a booster dose?
  10.  Should my child with an autoimmune disease get vaccinated?


*Updated recommendations from the CDC pertaining to boosters are outlined in Questions 9 & 10.



1. I have an autoimmune disease – which vaccine should I get?

Speak with your doctor to determine which vaccine is right for you; they will have a broader understanding of which vaccine suits you and your medical profile.

On January 31, 2022, the FDA approved Moderna’s COVID-19 vaccine. This is the second vaccine to gain full approval in the U.S. The Pfizer and BioNTech COVID-19 vaccine was approved by the FDA on August 23, 2021.

The application for full FDA approval requires ample clinical data from trials demonstrating high safety and efficacy ratings. Read the difference between approval and emergency use authorization on the FDA’s website.

Check out our vaccine comparison chart for details on scientific and research developments behind the world’s leading vaccines, from March 2020 – August 2022.



2. I have an autoimmune disease – is it safe for me to get the COVID vaccine?

From what the Global Autoimmune Institute has reviewed in the scientific literature in regards to COVID-19 vaccination and autoimmune disease, the evidence available at this point indicates that the benefit of COVID-19 vaccination outweighs the risk of side-effects.

The CDC also states that “COVID-19 vaccines may be administered to most people with underlying medical conditions.”

In regard to immunocompromised persons receiving a third vaccine dose, the CDC has stated that “there is limited information about the risks of receiving an additional primary shot of mRNA COVID-19 vaccine.” The safety, efficacy, and benefits of a third primary dose in those with compromised immune systems is being evaluated on an ongoing basis. Reactions to a third primary dose are similar to reactions after the two-dose primary series, and are typically mild to moderate in nature. “As with the two-dose primary series, serious side effects are rare, but may occur.”

The FDA has verified a list of rare adverse events, some of which can be found here.



3. I have an autoimmune disease – will the COVID-19 vaccine work for me?

The consensus has been that COVID-19 vaccine efficacy may be decreased for people who take immunosuppressant drugs, which includes many being treated for autoimmune disease. This was suspected by experts earlier in the pandemic but has been confirmed via clinical trials and real-world data including the following:

  • On May 2, 2021, researchers published the results of a retrospective study of 17 hospitals throughout Israel. The study included 152 patients who tested positive for COVID-19 after being fully vaccinated with the Pfizer vaccine (breakthrough cases) and required hospitalization. This study aimed to “characterize vaccinated patients with breakthrough COVID-19 requiring hospitalization and define the main risk factors associated with poor outcomes in this group.” Notably, 40% of breakthrough cases included patients who were immunocompromised. Data coming from Israel’s mass vaccination campaign parallel Phase 3 clinical trial data, supporting Pfizer vaccine’s 95% efficacy rate. That being said, efficacy was shown to be lower in those with multiple comorbidities and the immunocompromised. The most common causes of immunosuppression included chronic corticosteroid treatment, antimetabolite therapy, and anti-CD20 treatment (Rituximab, commonly used to treat rheumatoid arthritis, is an anti-CD20 biologic agent).
  • On August 6, 2021, a study was published that analyzed the immune response following COVID-19 vaccination in patients with autoimmune disease, focusing specifically on the effects of different immunosuppressive drugs on antibody development. Researchers used serum samples from 289 patients without autoimmune disease, who served as the control group, and 632 patients with autoimmune disease (including rheumatoid arthritisankylosing spondylitissystemic lupus erythematosus, and multiple sclerosis). Serum samples were collected from participants after their first or second dose of the COVID-19 vaccine (to include Johnson & Johnson, Pfizer, AstraZeneca, and Moderna). Seroconversion rates (speed of the body’s transition from viral infection to antibody presence in the body) and antibody titers were similar across autoimmune disease types and vaccine types included in the study, “suggesting that treatment with immunosuppressive medication, rather than the underlying autoimmune disease, is the main factor that influences immunogenicity of vaccines.”

For those with autoimmune disease who take immune system-altering medications, the American College of Rheumatology released a recommendation to delay taking such medications for one week after vaccination—under the direction of their doctor. Doing this may allow their immune systems to create a stronger antibody response and combat the drop in vaccine efficacy seen in those on immunosuppressants.



4. I take medications for my autoimmune disease – how will they interact with the COVID-19 vaccine?

The Washington University School of Medicine is conducting a study called COVaRiPAD (COVID-19 Vaccine Responses in Patients with Autoimmune Disease). The team just published research looking at the effect of immunosuppression on the efficacy of mRNA COVID-19 vaccines. They found that 88.7% of patients with chronic inflammatory conditions* (CID), including rheumatoid arthritis (28.5%), Crohn’s disease (16.5%), spondyloarthritis (15%), ulcerative colitis (13.5%), systemic lupus erythematosus (11.3%), multiple sclerosis (6.8%), and Sjögrens syndrome (6%), produced detectable antibodies in response to the vaccine.

Researchers found that immune responses varied depending on the medication being taken, which included glucocorticoids, antimetabolites, tumor necrosis factor inhibitors (TNFis), B-cell depleting therapy (BCDT), and Janus kinase inhibitors (JAKis). All CID participants continued use of their immunosuppressive medications during the study per their treating physician, except for 3 who held methotrexate (antimetabolite) within 1 week of immunization. Those taking BCDT (60%) and glucocorticoids (65%) had absent or numerically lower antibody levels after both vaccinations, while the other immunosuppressives did not generate much lower antibody levels when compared to those not taking the drugs.

It should be noted that the antibody levels in CID participants were one-third of the levels seen in the healthy controls. The researchers highlighted the difficulty of determining whether the levels achieved by those on immune-suppressing drugs are high enough to protect them from severe COVID-19 given that a minimum level of antibodies required for protection against COVID-19 has yet to be established. Nonetheless, evidence supporting that vaccination does elicit a response in those with compromised immune systems is still encouraging for a population that has a high risk of serious illness.

* Those with acquired or inherited immunocompromised conditions and those using systemic immunosuppression were excluded.

The primary recommendation from the American College of Rheumatology is to delay certain medications for one week after vaccination. These include:

  • Methotrexate
  • janus kinase (JAK) inhibitors – baricitinib (Olumiant), tofacitinib (Xeljanz), upadacitinib (Rinvoq)
  • Cyclophosphamide

Longer delays are recommended for biologics – abatacept (Orencia), rituximab (Rituxan).

It is recommended that you speak with your doctor about any medications you may be taking and how they may interact with the COVID-19 vaccine.



5. I have an autoimmune disease – am I at risk of experiencing a flare-up from the vaccine?

There is a risk that flare-ups may occur. That being said, it has been observed that people living with autoimmune and inflammatory conditions are at higher risk of experiencing severe symptoms from a COVID-19 infection. Due to this concern, the American College of Rheumatology has stated that “the benefit of COVID-19 vaccination outweighs any small, possible risks for new autoimmune reactions or disease flare after vaccination.”

This questionnaire study to come out of the Netherlands compiled the post-vaccination experience of 505 patients living with systemic autoimmune disease. Researchers compared the “tolerability of different COVID-19 vaccine types between patients with autoimmune diseases and healthy controls… [and assessed] the effect of COVID-19 vaccination on underlying disease activity. ” Severe adverse events occurred in 1% of patients. Moreover, COVID-19 vaccinations were not observed to trigger AD flares.

One study from Cedar’s Sinai Medical Center evaluated a longitudinal vaccine registry and reported that the Covid-19 vaccine was found to be safe for patients with immune-mediated inflammatory diseases, such as IBD. Adverse event frequency and type were similar to that of the general population. Moreover, authors have reassured IMID patients that the risk of adverse events is “likely not increased, and may be reduced, while on biologics.”

A research study published in Frontiers in Oncology evaluated COVID-19 vaccine (Pfizer and Moderna) safety in 566 immunocompromised patients including those with hematological malignancies (131), solid tumors (191), immune-rheumatological diseases (86), and neurological disease (158) including multiple sclerosis and generalized myasthenia. Overall, the “incidence of severe adverse events after vaccine administration was generally low and <3%.”

Prominent autoimmune disease organizations share a common consensus: that the benefits of the vaccine outweigh possible risks of experiencing new autoimmune reactions or flare-ups.

Read more about about post-vaccination flares in specific autoimmune diseases here.

Research on COVID-19 vaccine adverse events in autoimmune disease patients can be found here.



6. I have an autoimmune disease, was vaccinated, and have experienced side effects – what should I do now?

Speak with your doctor. They will have your complete medical history as well as current medical profile, and will be able to guide you through side effects you may be experiencing.

You can also submit your side effects to the Vaccine Adverse Effects Reporting System (VAERS). Scientists at the CDC and FDA monitor VAERS to decide which adverse events merit further investigation. There may be others experiencing similar side effects to you; submitting them to VAERS provides the best chance for the CDC and FDA to know and study side effects from the COVID-19 vaccine.


7. Where can I find clinical trial data on people with autoimmune diseases getting the COVID-19 vaccine?

People living with autoimmune disease and those on immunosuppressive therapies were not included in initial clinical trials for the COVID-19 vaccine. This is due to the fact these population groups can skew efficacy data.

That being said, the NIH is currently recruiting participants with autoimmune disease for a new clinical trial testing the Immunological Response to COVID-19 Vaccine in Patients With Autoimmune and Inflammatory Diseases Treated With Immunosuppressants and/or Biologics.

The National Institute of Arthritis and Musculoskeletal and Skin Diseases is also sponsoring an observational study on how a COVID-19 infection impacts patients with systemic autoimmune disease, particularly inflammation, the immune system and blood vessels. The study will also assess the response to potential antiviral treatments and vaccines for those living with autoimmune disease.

Yale and the National Institute of Allergy and Infectious Diseases (NIAID) are collaborating to evaluate the immune response to COVID-19 vaccination in immunodeficient patients, including those with autoimmune disease and undergoing treatment with anti-CD20 medications.



8. I have an autoimmune disease and had a covid-19 infection – should I still get both doses of the vaccine?

Speak with your doctor before getting the COVID-19 vaccine, as they may have recommendations regarding the timing and dosing of the COVID-19 vaccine that are specific to your medical profile.

As of September 2022, the CDC states that those who have been previously infected with COVID-19 should get vaccinated and receive a booster dose, as the effectiveness of the COVID-19 vaccine wanes over time. This is especially true for those who are immunocompromised.



9. I have an autoimmune disease – should I get a booster dose?

The CDC recently adjusted their language around COVID-19 vaccines, and recommendations now include staying up to date with COVID-19 vaccines for adequate protection. That being said, there are separate recommendations for those who are immunocompromised. “For people who are immunocompromised, the third primary dose is the final dose of the primary series of an mRNA COVID-19 vaccine. Boosters are shots that enhance or restore protection against COVID-19, which may have decreased over time” (5). 

Generally, living with an autoimmune disease does not necessarily mean you are immunocompromised. Oftentimes, certain medications and treatments may cause immunosuppression while reducing an autoimmune reaction. A consensus has not been made on the antibody threshold for adequate immunity against SARS-CoV-2. For this reason, it is recommended that you speak with your doctor about staying up to date with COVID-19 vaccines. 

This page details the COVID-19 immunization schedule per the CDC (accurate as of September 9, 2022).



On April 19, 2023, the CDC issued a blanket recommendation that everyone ages 6 years and older receive an updated bivalent mRNA COVID-19 vaccine, regardless of whether they were fully vaccinated with the monovalent primary series. Regarding immunocompromised persons, new recommendations allow for an additional bivalent vaccine dose. “This allows more flexibility for healthcare providers to administer additional doses to immunocompromised patients as needed.”

On October 3, 2022, the FDA published updated information on Evusheld, citing data that shows a 1,000 fold decrease in efficacy as a prophylaxis against the omicron subvariant.

On September 14, 2022, the CDC published their recommendation on the bivalent booster for those who are moderately to severely immunocompromised; they also cover eligibility for Evusheld.

On September 1, 2022, the CDC updated their recommendation for those 18+ to receive a Pfizer or Moderna bivalent booster. The updated booster targets the most recent Omicron subvariants, as well as the original SARS-CoV-2 strain.

On March 29, 2022, the CDC updated their recommendation to include a second booster dose for immunocompromised persons using the Pfizer or Moderna vaccine.

On January 7, 2022, the CDC updated their vaccine guidance for immunocompromised persons. It is now recommended that persons 12+ who are immunocompromised receive a booster dose. “If you are eligible for an additional primary shot, you should get this done before you get a booster shot.”

On December 16, 2021, the CDC recommended against the use of a second J&J dose following a J&J primary dose. Thrombosis with thrombocytopenia has been verified by the FDA and CDC as a rare but possible adverse event after receiving the J&J vaccine; given their recommendation on boosters in light of the Omicron variant, the CDC’s official stance now recommends an mRNA vaccine booster after the initial J&J primary dose. That being said, those wanting to receive two doses of a J&J vaccine may do so; it is recommended that you speak with your doctor beforehand.

On November 29, 2021, the CDC changed their recommendation on boosters in an effort to combat the Omicron variant. Adults “should” receive a booster, rather than “may” receive a booster 6 months after their Pfizer or Moderna primary series, or 2 months following their initial J&J vaccine.

On November 19, 2021, the CDC expanded booster eligibility for everyone over 18 years of age. Those who received a Pfizer or Moderna vaccine may receive a booster dose 6 months after their primary series.

Ahead of the CDC’s endorsement, an advisory committee to the CDC convened to discuss two new recommendations. Members voted 11-0 in favor of both recommendations:

#1 – A single COVID-19 vaccine booster dose is recommended for persons aged 18+ who received an mRNA COVID-19 vaccine primary series based on individual benefit and risk, at least 6 months after the primary series, under the FDA’s emergency use authorization.

#2 – A single COVID-19 vaccine booster dose is recommended for persons 50+ years who received an mRNA COVID-19 vaccine at least 6 months after the primary series under the FDA’s emergency use authorization. 

On October 26, 2021, the CDC updated their guidelines on COVID-19 vaccines for those who are “moderately and severely” immunocompromised. Those who received an mRNA vaccine for their primary series and received an additional dose of an mRNA vaccine, may receive a fourth COVID-19 booster dose at 6+ months. This fourth dose may be administered using a Moderna, Pfizer or Johnson & Johnson (J&J) vaccine. “In such situations, people who are moderately and severely immunocompromised may receive a total of four COVID-19 vaccine doses.”

If obtaining the Moderna vaccine for a third dose, one should receive a 50 microgram dose, followed by a fourth 50 microgram dose at 6+ months.

Those who are immunocompromised and received the J&J vaccine for their primary series should get a second COVID-19 vaccine. If the J&J primary dose is followed by a Moderna booster, it should measure 50 micrograms. Those who received a J&J vaccine for their primary series followed by either a second dose of the J&J, Moderna or Pfizer vaccine should not obtain a third dose at this time. Speak with your doctor regarding the timing of a fourth dose, as they are “best positioned to determine the appropriate timing of vaccination.”

On October 21, 2021, the CDC amended their EUA to include a booster recommendation for the Moderna and Johnson & Johnson vaccines. 

The Moderna vaccine has been endorsed for use as a booster vaccine at least 6 months after the primary series in the following populations:

  • those 65+ years in age
  • those 18+ in long-term care settings
  • those 18+ who have certain underlying medical conditions
  • those 18+ who work or live in high-risk settings

The Johnson & Johnson (J&J) vaccine has been recommended for persons 18+ years of age, 2 months after their primary dose. 

The CDC also endorsed a mix-and-match strategy for booster doses. Unlike the Moderna booster (which is a half dose at 50 micrograms), Pfizer and J&J booster doses will measure the same as the primary series. The ACIP, the advisory panel to the CDC, recommended that those who are immunocompromised and completing a primary series as well as an additional dose, should utilize vaccines from the same manufacturer. Those who are “moderately to severely” immunocompromised and received a J&J primary series, should receive a 50 microgram dose of the Moderna vaccine should they decide to mix-and-match between their first and second dose. Those who receive a third, 100 microgram dose of the Moderna vaccine due to their immunocompromised status, should not get a 4th booster shot from Pfizer or J&J at this time (1). 

On September 24, 2021, the CDC updated their recommendations for a booster dose of the Pfizer vaccine at least 6 months after a primary series for the following individuals: 

  • people 65 years and older and residents in long-term care settings 
  • people aged 50–64 years with underlying medical conditions people aged 18–49 years with underlying medical conditions may receive a booster shot based on their individual benefits and risks, and
  • people aged 18-64 years who are at increased risk for COVID-19 exposure and transmission because of occupational or institutional setting may receive a booster shot based on their individual benefits and risks. 

On August 12, 2021,  the FDA authorized the use of an additional dose of Pfizer-BioNTech and Moderna’s COVID-19 vaccines for those who are immunocompromised and may not have developed sufficient antibodies after a full dose of the COVID-19 vaccine. These patients include those who have received solid organ transplants, as well as “those who are diagnosed with conditions that are considered to have an equivalent level of immunocompromise.”

On August 13, 2021, the FDA authorized the use of a third dose of the Moderna vaccine as well, which measures 100 micrograms. This is the same dose as the first two of the primary series.

The NIH is currently holding a clinical trial on Booster Vaccine in Autoimmune Disease Non-Responders. This study will determine the antibody response of a booster dose in autoimmune disease patients who did not respond to an initial full dose of the COVID-19 vaccine. The trial includes participants living with one of five autoimmune diseases: rheumatoid arthritis, pemphigus, systemic lupus erythematosus, systemic sclerosis, or multiple sclerosis, and taking mycophenolate mofetil (MMF) or mycophenolic acid (MPA), methotrexate (MTX), or B cell-depleting drugs. These immunosuppressive therapies have been associated with low antibody production after the COVID-19 vaccine.



10. My child has an autoimmune disease – should they get vaccinated? 

This page details the COVID-19 immunization schedule for children starting at 6 months in age, including children who are immunocompromised.



As of June 16, 2023, the CDC recommends children 6 months-5 years receive a bivalent vaccine, with “optional additional bivalent booster doses for moderately or severely immunocompromised persons aged ≥6 months.” Children ≥6 months who are moderately or severely immunocompromised may receive ≥1 additional bivalent mRNA dose ≥2 months after their most recent bivalent mRNA dose.

On April 19 2023, the CDC updated guidelines for immunocompromised persons, including children 6 years and older. Their recommendation now allows for an additional bivalent vaccine dose on top of a primary bivalent mRNA COVID-19 dose; this is separate from a monovalent primary series. “This allows more flexibility for healthcare providers to administer additional doses to immunocompromised patients as needed… For young children, multiple doses continue to be recommended and will vary by age, vaccine, and which vaccines were previously received.”

On September 14, 2022, the CDC updated recommendations on a second booster for children ages 5-11 years, who received a Pfizer primary series. Children 12+ are also recommended to receive the Pfizer bivalent booster (4).

On May 20, 2022, the CDC updated their recommendation for children ages 5-11. Children within this age group should receive a third dose of the Pfizer vaccine at least 5 months after their second dose.

On February 22, 2022, the CDC updated their recommendation for time intervals between the first and second dose of the Moderna vaccine. Boys, especially those 12-39 years of age, are suggested to wait 8-weeks between their first and second dose. The CDC still recommends the original time interval of 4-weeks between Moderna doses for those who are moderately to severely immunocompromised.

On January 5, 2022, the CDC endorsed booster shots for children 12-17 years of age using the Pfizer vaccine, five months after the second dose of a primary series. This endorsement follows a 13-1 vote by the ACIP in favor of booster doses.

On January 3, 2022, the FDA authorized booster doses in children 12-15 years of age, five months after a primary series. Additionally, children 5-11 years of age with compromised immune systems may now receive a third dose of the Pfizer COVID-19 vaccine at least 28 days following a primary series.

The clinical trials conducted for the COVID-19 vaccine included different cohorts with groups split by age, including 16-25, 12-15, 6-11, 2-5, and 6 months to 2 years.

Pfizer-BioNTech was recently granted emergency use authorization in children ages 5-11 on October 29, 2021; vaccination in children 12+ was authorized on May 10, 2021. The FDA also granted EUA for a third dose of Pfizer’s vaccine in those 12+ “who have been determined to have certain kinds of immunocompromise” (2). This third shot is considered part of the primary series, and is different from a “booster.”

Pfizer’s clinical trials in children ages 5-11 and 12-15 did not include those with autoimmune disease; that being said, the vaccine demonstrated 91% and 100% efficacy, respectively, and robust antibody responses. In Pfizer’s clinical trial of 5-11 year olds, antibody responses were similar to those seen in 16-25 year olds, even though they received a low dose of the vaccine (two 10-microgram doses versus two 30-microgram doses for those 12+). The vaccine was also well-tolerated in both sets of age groups, with the most common adverse reactions being pain at the injection site, fatigue, headache, muscle pain, chills, and joint pain.

Read more about the CDC’s recommendation on vaccination in 5-11 year old pediatric populations, here. This CDC resource page discusses the benefits and potential risks of the vaccine in children 12-15 years of age, as well as recommendations, assessment, development, and evaluation of the Pfizer vaccine in children 12-15 years of age (3).

Last year, Creaky Joints released a statement regarding the COVID-19 vaccine in patients with juvenile arthritis, sharing that, “experts believe the Pfizer COVID-19 vaccine is safe for children who are immunocompromised or are taking a medication that affects the immune system.”

This review compiles the latest literature and recommendations on vaccination (generally) in children who are immunocompromised, including those with specific autoimmune diseases and being treated with immunosuppressive regimens. It is recommended that you speak with your child’s doctor regarding any medication they are taking for their autoimmune disease before getting the COVID-19 vaccine.



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The information shared on this page is accurate to the best of our knowledge. Please read resources provided by the CDC, WHO, and public health authorities to stay best informed, and seek professional medical advice for best practices pertaining to your medical plan.