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Vaccines

Vaccines and autoimmune diseases — can the immune system attack the body’s own tissues?

Sources: 15 · Article: 18 475 characters

Prof. Sucharit Bhakdi cites a review of 87 cases of hepatitis after COVID-19 vaccination, including 34 with no detected autoantibodies.

  • In the case described, he said, a possible explanation was an immune attack on the spike protein, rather than autoimmunity.
  • Bhakdi also describes cases of encephalitis diagnosed as autoimmune; he notes that its cause often cannot be determined without examining tissue.
  • The STOP NOP Association cites findings linking HPV vaccination with hypothyroidism, autoimmune thyroiditis, and serious autoimmune adverse events.

What the authors write

Stowarzyszenie STOP NOP

The STOP NOP Association cites findings suggesting a possible link between HPV vaccination and hypothyroidism and autoimmune thyroiditis.

„Our findings indicate a potential association between HPV vaccination and thyroid disease, particularly hypothyroidism and autoimmune thyroiditis.”Nasze wyniki wskazują na potencjalny związek między szczepieniem przeciwko HPV a chorobami tarczycy, w szczególności niedoczynnością tarczycy i autoimmunologicznym zapaleniem tarczycy
Lekarze ostrzegają! Szczepionka HPV – Ogólnopolskie Stowarzyszenie Wiedzy o Szczepieniach "STOP NOP"
Stowarzyszenie STOP NOP

The STOP NOP Association cites a study linking HPV4 vaccination with a serious autoimmune adverse event.

„This epidemiological study provides additional evidence supporting a significant association between HPV4 vaccination and cases of serious autoimmune adverse events (SAAEs).”To badanie epidemiologiczne dostarcza dodatkowych dowodów na poparcie istotnego związku między podawaniem szczepionki przeciwko HPV4, a przypadkami ciężkiego autoimmunologicznego zdarzenia niepożądanego (SAAE)
Lekarze ostrzegają! Szczepionka HPV – Ogólnopolskie Stowarzyszenie Wiedzy o Szczepieniach "STOP NOP"
Stowarzyszenie STOP NOP

In lawsuits concerning the Gardasil vaccine, plaintiffs alleged, among other things, that it caused autoimmune disorders.

„Among other things, plaintiffs alleged that the vaccine caused premature ovarian failure leading to infertility, POTS, autoimmune disorders, and other serious conditions. Merck, the manufacturer of the HPV vaccine, had the opportunity to prove the safety of its product in court, but instead chose to settle without an admission of liability and pay money. Gardasil Injury Settlement Several safety signals were recently identified in the U.S. Vaccine Adverse Event Reporting System (VAERS), supporting the accounts of Danish girls and U.S. lawsuits.”Powodowie zarzucali szczepionce m.in. przedwczesną niewydolność jajników prowadzącą do bezpłodności, POTS, zaburzenia autoimmunologiczne i inne poważne. Merck, producent szczepionki przeciw HPV, miał okazję udowodnić przed sądem bezpieczeństwo swojego produktu, ale wolał pójść na ugodę bez orzekania o winie i wypłacić pieniądze Gardasil Injury Settlement W amerykańskim systemie zgłaszania niepożądanych zdarzeń po szczepieniach (VAERS) ostatnio wykryto kilka sygnałów bezpieczeństwa, które potwierdzają historie duńskich dziewczyn i pozwów amerykańskich.
Lekarze ostrzegają! Szczepionka HPV – Ogólnopolskie Stowarzyszenie Wiedzy o Szczepieniach "STOP NOP"
Stowarzyszenie STOP NOP

The STOP NOP Association says the committee did not determine whether the childhood vaccination schedule is associated with autoimmune diseases.

„Questions about vaccines and chronic conditions that have not yet been answered Because there were not enough sufficiently rigorous clinical studies, conducted using sound methods and published in the medical literature, the IOM Committee studying the safety of the current childhood vaccination schedule was unable to determine whether or not the schedule is associated with the following chronic brain and immune system disorders and developmental disorders in children:24 autoimmune diseases; learning disorders; communication disorders; developmental disorders; intellectual disability; attention deficit disorder (ADD); antisocial disorders; tics and Tourette syndrome; febrile seizures; and epilepsy (seizure disorder).”Pytania o szczepienia i choroby przewlekłe, na które dotąd nie uzyskano odpowiedzi Z uwagi na brak wystarczająco rzetelnych badań klinicznych pod względem metodologii przeprowadzonych i opublikowanych w literaturze medycznej, Komisja IOM badająca bezpieczeństwo aktualnego kalendarza szczepień dla dzieci nie była w stanie stwierdzić, czy kalendarz ten jest, czy też nie jest powiązany z występowaniem następujących przewlekłych zaburzeń działania mózgu i układu odpornościowego oraz zaburzeń rozwojowych u dzieci:24 choroby autoimmunologiczne; zaburzenia uczenia się; zaburzenia komunikacji; zaburzenia rozwojowe; niepełnosprawność intelektualna; zespół deficytu uwagi (ADD); zaburzenia aspołeczne; tiki i zespół Tourette’a; drgawki gorączkowe i epilepsja (padaczka).
Szczepienia – poznaj ich ryzyko i skuteczność – Ogólnopolskie Stowarzyszenie Wiedzy o Szczepieniach "STOP NOP"
Stowarzyszenie STOP NOP

The STOP NOP Association links the deterioration in children’s health, which coincided with wider use of vaccines, to the occurrence of autoimmune diseases.

„Doctors and scientists have drawn attention to the decline in children’s health since the 1960s, which coincided with the increasingly widespread use of vaccines. Allergic diseases, including asthma, autoimmune diseases, diabetes, and many neurological disorders?”Lekarze i naukowcy zwracają uwagę na pogorszenie stanu zdrowia populacji dziecięcej od lat 60. ubiegłego wieku, co zbiegło się w czasie z wprowadzanymi coraz szerzej szczepieniami. Choroby alergiczne, w tym astma, choroby autoimmunologiczne, cukrzyca i wiele neurologicznych dysfunkcji ?
Dr n.med. Dorota Sienkiewicz „Bezpieczne szczepienia” – alternatywny kalendarz szczepień – Ogólnopolskie Stowarzyszenie Wiedzy o Szczepieniach "STOP NOP"
Hubert Czerniak

Hubert Czerniak claims that keeping a child in TH2 mode can lead to autoimmune diseases and therefore advocates starting vaccinations at six months of age.

„If an infection occurs in the body at that age, the ability to switch to the TH1 defense mode is greatly limited, or even impossible. If a child’s immune system remains only in TH2 mode, this leads to the development of autoimmune diseases. For this reason, we are campaigning for the first vaccinations to begin at six months of age.”miesiąca w organizmie wystąpi infekcja, wówczas możliwość przełączenia do trybu obronnego TH1, jest znacznie ograniczona, a nawet wręcz niemożliwa. Gdy odporność dziecka pozostanie jedynie w trybie TH2, prowadzi to do rozwoju chorób autoimmunologicznych. Z tego powodu walczymy, aby pierwsze szczepienia zaczynały się od szóstego miesiąca życia.
Wyleczyć nieuleczalne – autyzm
Prof. Sucharit Bhakdi

Prof. Sucharit Bhakdi describes autoimmune disease as the result of immune cells incorrectly recognizing the body’s own antigens.

„This, of course, should not be understood as an endorsement of adenovirus vector technology; virus-based vaccines against COVID-19 have caused severe adverse events on the same scale as mRNA vaccines [72]. 3.4 Induction of autoimmune disease 3.4.1 Background. We noted in the preceding chapter that autoimmune disease is caused by the emergence and proliferation of T and B lymphocytes that aberrantly recognize “self” antigens.”This is, of course, not to be understood as an endorsement of the adenovirus vector technology; the virus-based vaccines against COVID-19 have caused severe adverse events on the same scale as the mRNA vaccines [72]. 3.4 Induction of autoimmune disease 3.4.1 Background. We noted in the preceding chapter that autoimmune disease is caused by the emergence and proliferation of T- and B-lymphocytes which aberrantly recognize “self” antigens.
mRNA Vaccine Toxicity — M. Palmer i S. Bhakdi i in. (2023)
Prof. Sucharit Bhakdi

Prof. Sucharit Bhakdi cites a review of 87 cases of hepatitis after COVID-19 vaccination, 34 of which had no detected autoantibodies.

„Efe et al. [163] provided an overview of 87 cases of hepatitis after COVID-19 vaccination from multiple clinical centers. Among these, 34 did not exhibit any autoantibodies. The clinical course in these cases was somewhat milder than in those with evidence of autoimmunity, but otherwise the spectrum of clinical and pathological findings was similar.”Efe et al. [163] provided an overview of 87 cases of hepatitis after COVID-19 vaccination from multiple clinical centers. Among these, 34 did not exhibit any autoantibodies. The clinical course in these cases was somewhat milder than in those with evidence of autoimmunity, but otherwise the spectrum of clinical and pathological findings was similar.
mRNA Vaccine Toxicity — M. Palmer i S. Bhakdi i in. (2023)
Prof. Sucharit Bhakdi

Prof. Sucharit Bhakdi points out that, in the case of hepatitis described, a possible explanation was an immune attack on the spike protein, rather than autoimmunity.

„While their tentative diagnosis is autoimmune hepatitis, possibly drug-induced, the most likely cause is not autoimmunity but rather an immune attack against spike protein expressed by liver cells. We posit that, in the absence of evidence to the contrary, this explanation applies to most other cases of autoantibody-negative hepatitis as well, and probably also to many cases that show only a narrow spectrum of autoantibodies.”While their tentative diagnosis is autoimmune hepatitis, possibly drug-induced, the most likely cause is not autoimmunity but rather immune attack against spike protein expressed by liver cells. We posit that, in the absence of evidence to the contrary, this explanation applies to most other cases of autoantibody-negative hepatitis as well, and probably also to many cases that do show only a narrow spectrum of autoantibodies.
mRNA Vaccine Toxicity — M. Palmer i S. Bhakdi i in. (2023)
Prof. Sucharit Bhakdi

Prof. Sucharit Bhakdi says that encephalitis diagnosed as autoimmune has been reported after mRNA vaccination, but that its cause often cannot be determined without examining tissue.

„It is certainly reasonable to assume that in many such cases an unidentified autoantigen may have been causative. On the other hand, without histopathology, it will often be impossible to decide whether a given case of encephalitis was caused by an immune reaction against an unknown autoantigen or against the spike protein.”It is certainly reasonable to assume that in many such cases an unidentified autoantigen may have been causative. On the other hand, without histopathology, it will often be impossible to decide whether a given case of encephalitis was caused by an immune reaction against an unknown autoantigen or against the spike protein.
mRNA vaccines against COVID-19 and their effects on the central nervous system

Research from PubMed · Europe PMC

We selected 6 studies with the best, positive results. This is a selection, not a full review of all research.

Total number of studies on this topic in PubMed: 3 182.

A meta-analysis found no association between hepatitis B vaccination in adults and the onset of autoimmune diseases.

Aim of the study: To assess whether hepatitis B vaccination in adults is causally associated with autoimmune diseases. Such causation has been claimed mainly on the basis of case reports and uncontrolled studies, and a syndrome called 'Autoimmune/autoinflammatory Disorder Induced by Adjuvants' (ASIA) has been claimed to be linked to immunization, particularly hepatitis B vaccination.

Results: Overall, no association between hepatitis B vaccination and the onset of autoimmune diseases was seen. The overall odds ratio was 1.06, with 95% confidence limits of 0.93–1.21, and there was no significant heterogeneity. Only one study showed a significant excess risk between hepatitis B immunization and autoimmune disease. Despite multiple case reports, there is no reliable scientific evidence that hepatitis B vaccinations cause autoimmune diseases.

Autoimmune diseases after hepatitis B immunization in adults: Literature review and meta-analysis, with reference to 'autoimmune/autoinflammatory syndrome induced by adjuvants' (ASIA). · Vaccine 2018
Money for the studynot stated
Do the authors have ties to companies?not stated
Did a manufacturer help with the study?unknown
Type of studycombined analysis of many studies (meta-analysis)

“Not stated” does not mean nobody paid — the database does not always record it.

A large study found no increased risk of Guillain-Barré syndrome after vaccination in adults.

Aim of the study: The role of vaccination in the development of Guillain-Barré syndrome (GBS) is controversial, although cases of GBS have been reported following a wide range of vaccines. A nested case-control study was conducted between January 2011 and December 2015 in three Chinese cities.

Results: Among children and adults, adjusted odds ratios for GBS occurrence within 180 days following vaccination were 0.94 (95% CI 0.54–1.62) and 1.09 (95% CI 0.88–1.32), respectively. No increased risk of GBS was detected for vaccination against hepatitis B, influenza, hepatitis A, varicella, rabies, live polio, diphtheria, acellular pertussis, tetanus, measles, mumps, rubella, Japanese encephalitis, or meningitis. Adjusted odds ratios for GBS recurrence after vaccination among children and adults were 0.85 (95% CI 0.07–9.50) and 1.18 (95% CI 0.49–2.65), respectively. In this large retrospective study, we found no evidence of an increased risk of GBS or its recurrence among either children (≤18 years) or adults (>18 years) within 180 days of any vaccination, including influenza vaccination.

Vaccines and the risk of Guillain-Barré syndrome. · Eur J Epidemiol 2020
Money for the studygovernment, public institutions · Science Project of the Jiangsu Commission of Health, Science-Education Project of the Jiangsu Center for Disease Control and Prevention
Do the authors have ties to companies?not stated
Did a manufacturer help with the study?unknown
Type of studyobservation of people

“Not stated” does not mean nobody paid — the database does not always record it.

The shingles vaccine was similarly effective in people with autoimmune diseases and in other people.

Aim of the study: Individuals with autoimmune or immune-mediated diseases (AID) are more susceptible to infections and often experience worse outcomes if infected, underscoring the importance of vaccination. However, it remains unclear whether vaccine effectiveness (VE) differs between people with and without AID.

Results: For the herpes zoster trial, 169,054 vaccinated individuals were matched to the same number of controls, including 10,994 people with AID in each group. Herpes zoster VE was 68.73 (95% CI 55.75–77.91) in the AID group and 60.30 (55.59–64.52) in the non-AID group (VE ratio: 1.14, 95% CI 0.93–1.30). Across four influenza seasons (2015/2016–2018/2019), between 1,403,342 and 1,713,064 individuals were included, including between 56,662 and 78,320 people with AID. Influenza VE varied by outcome, season, and assumptions, but VE ratios remained close to one in most analyses (VE ratios: -0.92–3.77), with all CIs including one. There was no evidence that VE differed meaningfully between people with and without AID, after accounting for the included confounders. Both vaccines were similarly effective across groups, suggesting that VE is not reduced in patients with MS, IBD, or CIRD. Further research is needed to validate these findings for other AIDs and infections.

Influenza and herpes zoster vaccine effectiveness in autoimmune or immune-mediated diseases. · J Infect Public Health 2026
Money for the studyuniversity or foundation · Universitätsklinikum Jena, Universitätsklinikum Köln, Ruhr-Universität Bochum
Do the authors have ties to companies?not stated
Did a manufacturer help with the study?unknown
Type of studyobservation of people

“Not stated” does not mean nobody paid — the database does not always record it.

People with rheumatoid arthritis reported adverse events and hospitalizations at rates similar to those of healthy people.

Aim of the study: The COVID-19 vaccination in autoimmune diseases (COVAD) study aimed to assess short-term COVID-19 vaccination-related adverse events (AEs) in patients with RA.

Results: Of the 9462 complete respondents, 14.2% (n = 1347) had been diagnosed with RA; they had a mean (s.d.) age of 50.7 (13.7) years, 74.2% were women, and 49.3% were Caucasian. In total, 76.9% and 4.2% of patients with RA reported minor and major AEs, respectively. Patients with active and inactive RA had similar frequencies of AEs and hospitalizations. Overall, AEs were reported more frequently by recipients of BNT162b2 and mRNA-1273 and less frequently by recipients of BBV152, compared with the rest. Frequencies of major AEs and hospitalizations were similar across recipients of different vaccines. Patients receiving methotrexate and hydroxychloroquine reported fewer minor AEs than patients not taking these drugs. Compared with healthy controls (HCs) and patients with other AIRDs, patients with RA reported similar total AEs, overall minor AEs, and hospitalizations.

COVID-19 vaccination in autoimmune diseases (COVAD) study: vaccine safety and tolerance in rheumatoid arthritis. · Rheumatology (Oxford) 2023
Money for the studycompany together with others · Arthritis UK, AstraZeneca, Eli Lilly
Do the authors have ties to companies?not stated
Did a manufacturer help with the study?YES
Type of studyobservation of people
Participants9 462

“Not stated” does not mean nobody paid — the database does not always record it.

In people with weakened immune systems, including those with autoimmune diseases treated with immunosuppressants, COVID-19 vaccination was associated with a lower risk of severe outcomes from infection, and studies found no consistent increase in disease flares.

Aim of the study: Immunocompromised individuals face elevated risks of severe COVID-19, yet vaccination guidance for these populations continues to evolve.

Results: Most studies had short follow-up periods, likely reflecting higher-end estimates of vaccine effectiveness. Given moderate certainty of benefit and low certainty of harm, the panel strongly recommends the 2025–2026 COVID-19 vaccine for all immunocompromised individuals aged ≥6 months, with timing tailored to immunosuppressive therapy, clinical stability, and community transmission levels. Additional strategies—including vaccination of household contacts and early access to antivirals—remain essential. Research priorities include defining immune correlates of protection, evaluating how long protection lasts, optimizing vaccine timing, and improving real-world effectiveness and safety data.

IDSA 2025 Guidelines on the Use of Vaccines for the Prevention of Seasonal COVID-19 Infections in Immunocompromised Patients. · Clin Infect Dis 2026
Money for the studyuniversity or foundation · Infectious Diseases Society of America
Do the authors have ties to companies?not stated
Did a manufacturer help with the study?unknown
Type of studyreview of many studies

“Not stated” does not mean nobody paid — the database does not always record it.

Guidelines recommend COVID-19, influenza, and RSV vaccination for immunocompromised people, including patients with autoimmune diseases who take immunosuppressive drugs.

Aim of the study: Respiratory viruses—including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or COVID-19), respiratory syncytial virus (RSV), and influenza—pose significant risks to immunocompromised patients, who have weaker vaccine responses and higher rates of illness.

Results: Gaps remain in research on immunogenicity, durability, and clinical effectiveness, particularly for patients receiving B-cell-depleting therapies or in the early period after transplantation. Priority areas include defining correlates of protection, optimizing vaccine schedules, evaluating high-dose or adjuvanted formulations, and improving real-world effectiveness and safety data. Equity and access strategies are essential to ensure uptake among vulnerable populations. These guidelines aim to support evidence-based decision-making and highlight the need for coordinated research across multiple viruses to inform tailored vaccination strategies for immunocompromised individuals.

IDSA 2025 Guidelines on the Use of Vaccines for the Prevention of Seasonal COVID-19, Influenza, and RSV Infections in Immunocompromised Patients. · Clin Infect Dis 2026
Money for the studyuniversity or foundation · Infectious Diseases Society of America
Do the authors have ties to companies?not stated
Did a manufacturer help with the study?unknown
Type of studyother

“Not stated” does not mean nobody paid — the database does not always record it.

Perspectives and opinion materials

The content below presents the authors’ opinions, interpretations and hypotheses. It is not treated as equal to scientific studies and systematic reviews.

Orthomolecular Medicine News Service Opinion material
„Unfortunately, today older children and adults are now susceptible to mumps, rubella, and measles after their vaccine immunity has worn off. The solution? More vaccines! More and more vaccinations. The idea of combining several vaccines into one shot was now well established. But there was also a feeling that vaccine manufacturers followed the philosophy: “If we can, we will.” New vaccines are approved at an astonishing rate. There are several combinations of three, and even five, vaccines in one shot, justified as a way to avoid the “pin cushion” effect inflicted on infants.”Unfortunately, today older children and adults are now susceptible to mumps, rubella and measles after their vaccine immunity has worn off. The solution? More vaccines! More and more vaccinations The concept of combining several vaccines into one shot was now well established. But also there was a feeling that vaccine manufacturers had the philosophy of "If we can, we will. New vaccines are approved at an astonishing rate. There are several combinations of three, and even five, vaccines in one shot justified by avoiding the "pin cushion" effect inflicted on infants.
VACCINATIONS: To Be or Not to Be
Orthomolecular Medicine News Service Opinion material
„Those with antibody levels to squalene had a high incidence of an autoimmune disease. Those without did not. The industry’s objection to this study was widely and vehemently publicized.”Those with antibody levels to squalene had a high incidence of an autoimmune disease. Those without, did not. The industry's objection to this study was widely and vehemently publicized.
VACCINE ADJUVANTS AND EXCIPIENTS: Know what else comes through the needle?
Orthomolecular Medicine News Service Opinion material
„The paper, which found only 31 studies worthy of inclusion out of a massive 5,700 screened, concluded that there was only good evidence for moderate flu vaccine efficacy in healthy adults, and no real evidence of protection in those over 65 years, or, for that matter, in children.”The paper, which found only 31 studies worthy of inclusion out of a massive 5,700 screened, concluded that there was only good evidence for moderate flu vaccine efficacy in healthy adults, and no real evidence of protection in those over 65 years, or for that matter in children.
Flu Vaccine: No Good Evidence

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