The Science on Autism and Vaccines Is Not Settled: What Studies Are Missing

For too long we’ve been told that, without doubt, childhood vaccines are safe—but in reality, we do not know.

Illustration by The Epoch Times/Shutterstock

Like many physicians, I was taught early in my training that any link between vaccines and autism had been completely disproven—that “the science is settled” and no longer open for debate. I repeated that message with confidence for years. But when I began researching for my book, “Between a Shot and a Hard Place,” I set aside assumptions and took an unbiased look at the data myself.

What I found wasn’t reassuring. It wasn’t the robust body of evidence putting the question to rest. Instead, I found a surprisingly limited collection of studies—filled with narrow designs and major gaps. As a board-certified pediatrician trained at top institutions, I expected certainty. What I found was an unsettled and incomplete landscape—one that calls not for dogma, but for open scientific inquiry and nuance.

Let me be clear: I am not claiming that vaccines cause autism. I am saying, with humility and urgency, that we do not know. And the truth is, no one can say with confidence that we do.

That’s the problem.

The Scope of the Problem

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition. While some children are only mildly affected, many face significant challenges with speech, motor skills, and daily functioning. The spectrum is wide—and growing.

According to the CDC’s latest numbers, one in 31 children in the United States is now diagnosed with autism. In California, the numbers are even higher: one in every 12 1/2 boys. While it’s true that changes in diagnostic criteria and increased awareness have contributed to the rise, they don’t explain the increase in severe cases.

Nearly two-thirds of children with autism today have borderline or profound intellectual disability—a rate that’s higher than in decades past. This is a public health crisis. One we cannot solve if we refuse to ask the hard questions about what may be contributing to it.

The Illusion of Certainty

We’ve been told, repeatedly, that the question has been answered. That the debate is over. That it has been “thoroughly studied.”

When I began the research for my book, I expected to find a library of randomized controlled trials comparing vaccinated and unvaccinated children, robust epidemiological data tracking the CDC vaccine schedule’s long-term neurological impacts, and studies evaluating dose timing, adjuvant combinations, and biologically plausible mechanisms.

Instead, I found a tiny pool of repetitive studies, nearly all examining the MMR (measles, mumps, and rubella) vaccine or thimerosal—the mercury component of vaccines—a preservative phased out of most vaccines 20 years ago. The most frequently cited studies—Madsen (2002), DeStefano (2013), Hviid (2019)—do not compare vaccinated children with unvaccinated children. They compare children who received one type of vaccine with those who received other vaccines.

It’s like studying whether smoking causes cancer by comparing those who smoke filtered cigarettes with those who smoke unfiltered ones—without ever comparing either group with nonsmokers.

The lack of rigor here is not subtle. It is foundational.

I fully expected to uncover a vast body of clinical trials and mountains of epidemiological data confirming what I’d always been told: that vaccines do not cause autism. I assumed this question had been thoroughly answered and backed by modern science. But what I found instead left me in disbelief.

There were no large, comprehensive studies evaluating all vaccines on the CDC schedule and their potential link to autism. The research that I had been taught existed simply wasn’t there.

In an effort to better understand, I turned to two of the most well-known vaccine experts—Drs. Peter Hotez and Paul Offit—reading their works. But the only studies referenced were the usual handful—focused on MMR, thimerosal, and a DeStefano study that compared antigen counts—not actual vaccine exposure—among children who had already been vaccinated—alongside a few older citations and CDC website links.

There was no reference to any other data or studies addressing hepatitis B, DTaP, Hib, IPV, PCV, rotavirus, RSV, influenza, Vitamin K, hepatitis A, varicella, or any combinations of these vaccines in relation to autism in children.

What Remains Unstudied

The claim that “the science on vaccines and autism is settled” or that “the relationship has been debunked” is not backed by comprehensive, independent research. Instead, I found:

• No large, long-term randomized controlled trials comparing fully vaccinated with fully unvaccinated children.
• No meaningful research examining the long-term effect of multiple vaccines given at once, which is how children typically receive them.
• Minimal investigation into aluminum adjuvants, despite known neuroinflammatory potential in animal and cellular studies.
• No studies evaluating the safety of the full CDC vaccine schedule as it is actually administered, with its current timing and combination of doses.
• Minimal to no long-term autism research on most childhood vaccines aside from MMR—including hepatitis B, hepatitis A, rotavirus, PCV (pneumococcal conjugate vaccine), varicella, DTaP (diphtheria, tetanus, and pertussis), and polio.
• No long-term safety data on the most recently added vaccines, such as COVID-19, RSV (respiratory syncytial virus), or new combination vaccines—each introduced without long-term post-marketing surveillance in diverse populations.

The Institute of Medicine—a leading independent body that advises the government on medical and public health issues—published a report in 2013 that showed the federally recommended birth-to-6-year-old child vaccine schedule had not been fully scientifically evaluated. The report further stated that there was not enough scientific evidence for physician committees to determine if the childhood vaccine schedule is or is not associated with the development of a number of brain and immune system disorders prevalent among children today, including autism. The admission underscores the reality that the full vaccine schedule, as administered in real-world settings, lacks the comprehensive scientific scrutiny many assume it has received.

This isn’t a fringe opinion. It’s in the official literature. But the public never hears it.

Red Flags and Suppressed Stories

A 2014 review published in Pediatrics—intended to summarize the safety of childhood vaccines—mentions autism nine times. But nearly all references are confined to reiterating the now-familiar claim that the MMR vaccine is not associated with autism, largely echoing previous conclusions. However, buried within the paper is a reference to a 2010 study by Gallagher and Goodman, which found a significantly increased risk of autism in boys who received the hepatitis B vaccine within the first month of life—a threefold increase compared with those who received it later or not at all. Despite the weight of that finding, it received minimal critical discussion.

Dr. William Thompson is a senior CDC scientist who became a whistleblower in 2014. In his testimony, he revealed that critical data showing an increased risk of autism in African American boys vaccinated before 36 months had been omitted from a CDC study he coauthored. Thompson later stated: “I regret that my coauthors and I omitted statistically significant information.”

This should have sparked a public investigation. It didn’t.

In my practice, I have heard the same story over and over again. A healthy, happy baby receives vaccines—often multiple at once. Within hours or days, something shifts. Speech stalls. Eye contact fades. They stop responding to their name. The parents are terrified. They know something is wrong. But when they seek help, they are dismissed—told it’s coincidence, that it couldn’t possibly be the vaccine. They’re often labeled “anti-vax” simply for asking the question. But these parents are not anti-vaccine. In fact, quite the opposite: They took their child in for vaccines, believing they were doing the right thing.

They trusted the system. They followed the schedule. And when their child changed—sometimes overnight—they did what any parent would do: They looked for answers. In their view, a vaccine triggered a serious reaction. Maybe they’re right. Maybe it’s coincidence. But either way, these stories deserve to be heard. Dismissing them outright is not science—it’s dogma.

True science requires curiosity. It demands that we follow data and reports—even when it’s uncomfortable. These stories are not just anecdotes. They are observations. They are data points. The sheer number of parents reporting nearly identical timelines and symptoms should give us pause—not because it proves causation—but because it warrants deeper, independent investigation. Silencing these voices doesn’t protect science. It undermines it.

What Real Science Requires

Science is never settled. It evolves. It questions. It challenges assumptions. It refines its conclusions as new information becomes available.

If we want truth, we need to:

• Conduct independent, prospective longitudinal studies comparing vaccinated and unvaccinated children, using standardized autism assessments.

These studies are long overdue and could be conducted both retrospectively and prospectively in ethically sound ways. Retrospective analyses could leverage existing large-scale health databases—such as the Vaccine Safety Datalink, insurance claims, electronic medical records, or vaccine registries—to compare outcomes between fully vaccinated, partially vaccinated, and unvaccinated children—while adjusting for potential confounders.

Prospectively, open-label trials could be designed in which parents who have already chosen not to vaccinate—or to delay or selectively vaccinate—are observed alongside vaccinated children, with both groups followed over time using consistent and standardized neurodevelopmental assessments. No child would be denied care, and no family would be randomized against their will—eliminating the common ethical objections to such comparisons.

• Study the timing, grouping, and frequency of vaccine administration.
• Evaluate the long-term effects of adjuvants, preservatives, and biologically active ingredients on neurodevelopment.
• Account for genetic susceptibilities—including mutations, auto-immune conditions, and mitochondrial disorders—that may make some children more vulnerable.
• Listen to parents and investigate reasonable reports as valid observational data.
• Remove financial conflicts of interest from vaccine safety research and ensure full data transparency.

A Call for Integrity

I’m not anti-vaccine. I offer vaccines in my practice. I believe in protecting children from serious diseases. But I also believe in honesty, humility, and ethics.

What I cannot support is blind adherence to a narrative that refuses to admit what it hasn’t studied. I cannot support a system that silences dissent instead of answering it with better science.

We don’t need censorship. We need open discussion, debate, and nuance. We need a medical culture that welcomes questions, honors informed consent, and embraces complexity.

We owe our children nothing less.

Because when the health of millions of kids is on the line, we cannot afford to be wrong. And the only way to be right is to admit what we don’t know.

No, the science is not settled.

Views expressed in this article are the opinions of the author and do not necessarily reflect the views of The Epoch Times. Epoch Health welcomes professional discussion and friendly debate. To submit an opinion piece, please follow these guidelines and submit through our form here.