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The long-running debate over whether vaccines cause autism reflects an “epistemic crisis” in medical science — not a dispute over scientific facts, according to a new preprint by Children’s Health Defense scientists and their colleagues.
Existing epidemiological studies — studies on how often diseases occur in different groups of people and why — are designed to examine whether vaccines cause neurodevelopmental injuries in the general childhood population.
These studies can’t capture the effects of vaccines on subgroups — like children with mitochondrial dysfunction who may be more vulnerable to injuries from vaccines.
Typically, these studies don’t examine any of the biological markers — mitochondrial function, oxidative stress and immune system dysregulation — through which vaccines might cause harm.
The failure to recognize this possible connection points to a deeper structural problem in vaccine research, which routinely uses findings from epidemiological studies to settle questions those studies were never designed to answer.
Mitochondrial vulnerability, inherited and detectable at birth, means affected children may respond differently to environmental triggers, including vaccines. It also means vaccines may not pose the same risk for all children.
Co-author Karl Jablonowski, Ph.D., summarized the findings:
“Population studies that do not probe mitochondrial health are not going to find the association. It’s like looking for microscopic life with a telescope. Population-level studies that were never designed to detect an association are — not surprisingly — not going to detect an association.
“If you have mitochondrial dysfunction (known or unknown), the sum total of our existing, population-level evidence-based vaccine-safety scientific literature is not about you.”
The authors of the study don’t claim that “vaccines cause autism.” Instead, they argue that an integrated framework must investigate the “vaccine-mitochondria-autism” hypothesis.
Mainstream research on autism and vaccines ignores key questions
According to the authors of the preprint, public discourse on the vaccine-autism link has been reduced to a simple “yes/no” question, and mainstream public messaging has collapsed multiple distinct questions into a single statement: “vaccines do not cause autism.”
The vaccine-autism controversy has been distorted because researchers, regulators and media outlets routinely conflate four separate issues:
- Whether vaccines increase autism rates in the general childhood population.
- Whether vaccines can trigger regression into autism in biologically vulnerable children.
- How many children with autism exhibit mitochondrial dysfunction or related metabolic abnormalities.
- How legal structures, funding systems, peer review and media narratives shape what questions are asked and answered.
Mainstream research has largely addressed only the first question — and even then, incompletely, by focusing on individual vaccines rather than the full childhood vaccination schedule. Most of the research to date hasn’t even considered the other three questions.
The authors propose that in order to answer the question, “Do vaccines cause autism?” researchers use an integrated framework that looks at health patterns across large groups of people, while also zooming in on the specific underlying biological causes of disease in smaller, more targeted groups of patients.
“The integration is not a methodological luxury; it is a logical necessity,” they write.
Mitochondrial dysfunction may make kids more vulnerable to injury from vaccine ingredients
Research shows that about 5% of children with autism meet the formal criteria for mitochondrial dysfunction, and another 30% to 80% show subclinical mitochondrial abnormalities.
According to the paper, in children with autism, the mitochondria — the parts of cells that generate energy — aren’t working properly.
This means the brain isn’t getting enough energy to carry out basic functions like firing neurons, maintaining connections between brain cells and clearing away unnecessary synapses.
A synapse is a microscopic space that separates two neurons. Although it’s only a few tens of nanometers thick, it plays a crucial role in transmitting information.
Typically, the brain naturally eliminates excess synapses as it matures, a process that requires a lot of energy. When mitochondria are underperforming, this “pruning” becomes inefficient, leaving too many synaptic connections in place.
That imbalance can make it harder for the brain to regulate its own activity.
Dysfunctional mitochondria leak more electrons, which react with oxygen to create harmful molecules called reactive oxygen species. In children with autism, this happens at higher-than-normal rates, which overwhelms the body’s natural defenses.
One of those defenses is glutathione, an antioxidant. When glutathione is overwhelmed, damage to fats, proteins and the mitochondria’s own DNA can occur. This kind of damage has consistently been found in brain tissue and blood samples from children with autism.
This type of oxidative damage triggers the brain’s immune cells to release inflammatory signals, creating a state of chronic, low-grade brain inflammation. The inflammation interferes with how synapses form and adapt, which is thought to contribute to core autism features like social difficulties and repetitive behaviors.
At the same time, the stressed mitochondria accumulate misfolded proteins, which activate a built-in cellular rescue system designed to clean up the damage.
In healthy cells, this works fine. But in children with autism, the underlying mitochondrial defects are persistent enough that this rescue system gets overwhelmed and can’t keep up — so the damage continues during critical windows of early brain development, when the stakes are highest.
The authors also highlight evidence suggesting mitochondrial vulnerability may exist prenatally or at birth. For children who have this vulnerability, exposure to environmental stressors — including toxic ingredients in vaccines — during early development may exacerbate their condition and could trigger disorders such as autism.
The authors develop a methodology for connecting mitochondrial biology and vaccine component toxicology with epidemiology in order to investigate this causal link.
How do vaccine ingredients affect mitochondrial function?
The paper also cites substantial evidence from laboratory and experimental studies into the effect of vaccine components on mitochondrial function.
Research shows that aluminum adjuvants, lipid nanoparticles used in mRNA vaccines, thimerosal preservatives, and live viruses may affect mitochondrial functioning, oxidative stress and inflammatory signaling.
Individual case studies, such as the 2006 Hannah Poling case, have demonstrated how, following vaccination, a child with preexisting mitochondrial vulnerability who was exposed to many of these toxins experienced a metabolic crisis followed by developmental regression.
Public doesn’t get the full picture on possible link between vaccines, autism
Health agencies, advocacy groups, and media routinely translate cautious research findings in scientific papers into sweeping categorical statements — like “vaccines do not cause autism” — that go beyond what the underlying studies actually show.
The result, the authors argue, is an institutional pattern of overclaiming that erodes public trust and makes honest communication harder to restore.
On top of that, there’s the 1986 National Childhood Vaccine Injury Act, which shields vaccine makers from standard lawsuits. Without lawsuits, the public never gets access to internal corporate records that might shed more light on manufacturers’ studies and data.
As a result, the publicly available evidence showing that vaccines are safe appears more reassuring than it might otherwise be if there were a different process for assessing vaccine injuries.
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‘The scientific path forward is clear and urgent’
The preprint was published amid renewed national attention to vaccine policy and autism research, including discussions about possible environmental contributors to autism spectrum disorder.
The Centers for Disease Control and Prevention (CDC) has launched a “massive testing and research” initiative into the root causes of autism and the National Institutes of Health launched an autism research program.
In November 2025, the CDC updated its webpage on autism and vaccines to state that there is no evidence supporting the claim that vaccines don’t cause autism.
Autism diagnoses in the U.S. have risen sharply over the past two decades. The CDC estimates that as of 2022, 1 in 31 8-year-olds — more than 3.2% — are diagnosed with autism, a sharp rise from 1 in 36 kids just two years prior.
The authors say that better and broader diagnostic tools aren’t enough to explain the trend, and that the magnitude of the change requires further study of environmental factors that may trigger autism in some children.
“The scientific path forward is clear and urgent,” they conclude. The “current disconnected evidentiary domains” must be abandoned.
They argue for prospective studies focused on children with mitochondrial vulnerabilities — because existing evidence leaves unresolved questions about subgroup-specific risks.
They wrote:
“Until such studies are completed, intellectual honesty requires acknowledging that the vaccine-mitochondria-autism hypothesis in susceptible individuals remains a credible and testable explanation for a portion of the observed rise in ASD prevalence. The current absence of definitive proof does not constitute proof of absence.”
Related articles in The Defender
- RFK Jr. Launches ‘Massive Testing and Research’ Into Autism Epidemic
- ‘Honesty at Last’: CDC Says ‘No Evidence’ to Support Claim that Vaccines Don’t Cause Autism
- Thimerosal in Vaccines May Contribute to Autism Severity, New Analysis Shows
- Scientists Publish ‘Map’ for How Aluminum in Vaccines Can Cause Brain Injury That Triggers Autism
- Thimerosal in Vaccines May Contribute to Autism Severity, New Analysis Sho
- Kids, Vaccines and Autism: Will a New Legal Strategy End the Decades-long Battle for Truth and Justice?
