White puzzle pieces interconnected with one piece labeled "vaccine"

COVID Vaccine & Autoimmune Disease FAQ

As access to the vaccine has increased, the team at Global Autoimmune Institute has 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 our answers to our most frequently asked questions!

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 August 23, 2021, Pfizer and BioNTech’s COVID-19 vaccine was approved by the FDA, making it the first and only vaccine in the U.S. with full approval. 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.

To learn more about the scientific and research developments behind the world’s leading vaccines, check out our vaccine comparison chart, updated weekly!

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

I have an autoimmune disease - will the Covid 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.


In August 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.”

I take medications for my autoimmune disease - how will they interact with the COVID 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.

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.”

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.”

This questionnaire study to come out of the Netherlands compiled the post-vaccination experience of 505 patients living with systemic autoimmune disease. Moreover, they compared the “tolerability of different COVID-19 vaccine types between patients with autoimmune diseases and healthy controls… [and] assess[ed] the effect of COVID-19 vaccination on underlying disease activity. ” Severe adverse events occurred in 1% of patients.

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.

To learn more about post-vaccination reactions in specific autoimmune diseases, visit our COVID-19 and Autoimmune Disease News page.

I have an autoimmune disease, was vaccinated, and have experienced side effects - what do 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.

Where can I find clinical trial data on people with autoimmune diseases getting the COVID 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.

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. That being said, the CDC states that even those who have been previously infected with Covid-19 should get both doses of the vaccine.

I have an autoimmune disease - should I get a booster dose?

On August 12, 2021, the FDA authorized the use of an additional dose of the Pfizer vaccine for those who are immunocompromised. The FDA added that a booster dose would also be available to “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 another dose of the Moderna vaccine as well.

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. It is still unclear what the antibody threshold is for adequate immunity against SARS-CoV-2.

For this reason, it is recommended that you speak with your doctor regarding a booster dose of the COVID-19 vaccine. The timing of and your immune response after a full dose, medications you may be taking, and other aspects of your medical profile will play a role in whether you need an additional dose.


On September 24, 2021, the CDC updated their recommendations to include the following:

  • people 65 years and older and residents in long-term care settings should receive a booster shot of Pfizer-BioNTech’s COVID-19 vaccine at least 6 months after their Pfizer-BioNTech primary series,
  • people aged 50–64 years with underlying medical conditions should receive a booster shot of Pfizer-BioNTech’s COVID-19 vaccine at least 6 months after their Pfizer-BioNTech primary series,
  • people aged 18–49 years with underlying medical conditions may receive a booster shot of Pfizer-BioNTech’s COVID-19 vaccine at least 6 months after their Pfizer-BioNTech primary series, 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 of Pfizer-BioNTech’s COVID-19 vaccine at least 6 months after their Pfizer-BioNTech primary series, based on their individual benefits and risks.

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.

My child has an autoimmune disease - should they get vaccinated? 

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 for use in children ages 12-15. Their clinical trial in children ages 12-15 did not include those with autoimmune disease; that being said, the results were positive in that the vaccine demonstrated 100% efficacy and a robust antibody response. The vaccine was also well-tolerated, with the most common adverse reactions being pain at the injection site, fatigue, headache, muscle pain, chills, and joint pain.

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 (1).

Earlier this 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.”

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. Because the COVID-19 pandemic is rapidly evolving, as is the scientific community’s understanding of this virus, information and insights are constantly updating. Please read resources provided by the CDC, WHO, and public health authorities to stay informed, and seek professional medical advice for best practices pertaining to your medical plan.


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