Let’s start with one unambiguous fact: More children are diagnosed with autism today than in the early 1990s.

According to a sweeping 2000 analysis by the Centers for Disease Control and Prevention, a range of 2–7 per 1,000, or roughly 0.5 percent of US children, were diagnosed with autism in the 1990s. That figure has risen to 1 in 35 kids, or roughly 3 percent.

The apparent rapid increase caught the attention of people like Robert F. Kennedy Jr., who assumed that something had to be changing in the environment to drive it. In 2005, Kennedy, a lawyer and environmental activist at the time, authored an infamous essay in Rolling Stone that primarily placed the blame for the increased prevalence of autism on vaccines. (The article was retracted in 2011 as more studies debunked the vaccine-autism connection.) More recently, he has theorized that a mysterious toxin introduced in the late 1980s must be responsible.

Now, as the nation’s top health official leading the Department of Health and Human Services, Kennedy has declared autism an “epidemic.” And, in April, he launched a massive federal effort to find the culprit for the rise in autism rates, calling for researchers to examine a range of suspects: chemicals, molds, vaccines, and perhaps even ultrasounds given to pregnant mothers.

“Genes don’t cause epidemics. You need an environmental toxin,” Kennedy said in April when announcing his department’s new autism research project. He argued that too much money had been put into genetic research — “a dead end,” in his words — and his project would be a correction to focus on environmental causes. “That’s where we’re going to find an answer.”

But according to many autism scientists I spoke to for this story, Kennedy is looking in exactly the wrong place.

Autism is a complex disorder with a range of manifestations that has long defied simple explanations, and it’s unlikely that we will ever identify a single “cause” of autism.

But scientists have learned a lot in the past 50 years, including identifying some of the most important risk factors. They are not, as Kennedy suggests, out in our environment. They are written into our genetics. What appeared to be a massive increase in autism was actually a byproduct of better screening and more awareness.

“The way the HHS secretary has been walking about his plans, his goals, he starts out with this basic assumption that nothing worthwhile has been done,” Helen Tager-Flusberg, a psychologist at Boston University who has worked with and studied children with autism for years, said. “Genes play a significant role. We know now that autism runs in families… There is no single underlying factor. Looking for that holy grail is not the best approach.”

Doctors who treat children with autism often talk about how they wish they could provide easy answers to the families. The answers being uncovered through genetics research may not be simple per se, but they are answers supported by science.

Kennedy is muddying the story, pledging to find a silver-bullet answer where likely none exists. It’s a false promise — one that could cause more anxiety and confusion for the very families Kennedy says he wants to help.

The autism “epidemic” that wasn’t

Autism was first described in 1911, and for many decades, researchers and clinicians confused the social challenges and language development difficulties common among those with the condition for a psychological issue. Some child therapists even blamed the condition on bad parenting.

But in 1977, a study discovered that identical twins, who share all of their DNA, were much more likely to both be autistic than fraternal twins, who share no more DNA than ordinary siblings. It marked a major breakthrough in autism research, and pushed scientists to begin coalescing around a different theory: There was a biological factor.

At the time, this was just a theory — scientists lacked the technology to prove those suspicions at the genetic level. And clinicians were also still trying to work out an even more fundamental question: What exactly was autism?

For a long time, the criteria for diagnosing a person with autism was strictly based on speech development. But clinicians were increasingly observing children who could acquire basic language skills but still struggled with social communication — things like misunderstanding nonverbal cues or taking figurative language literally. Psychologists gradually broadened their definition of autism from a strict and narrow focus on language, culminating in a 2013 criteria that included a wide range of social and emotional symptoms with three subtypes — the autism spectrum disorder we’re familiar with today.

Along the way, autism had evolved from a niche diagnosis for the severely impaired to something that encompassed far more children.

It makes sense then, that as the broad criteria for autism expanded, more and more children would meet it, and autism rates would rise. That’s precisely what happened. And it means that the “epidemic” that Kennedy and other activists have been fixated on is mostly a diagnostic mirage.

Historical autism data is spotty and subject to these same historical biases, but if you look at the prevalence of profound autism alone — those who need the highest levels of support — a clearer picture emerges. (There is an ongoing debate in the autism community about whether to use the terminology of “profound autism” or “high support needs” for those who have the most severe form of the condition.) In the ’80s and ’90s, low-support needs individuals would have been less likely to receive an autism diagnosis given the more restrictive criteria and less overall awareness of the disorder, meaning that people with severe autism likely represented most of the roughly 0.5 percent of children diagnosed with autism in the 1990s. (One large analysis from Atlanta examining data from 1996 found that 68 percent of kids ages 3 to 10 diagnosed with autism had an IQ below 70, the typical cutoff for intellectual disability.)

By 2025, when about 3 percent of children are being diagnosed with autism, about one in four of those diagnosed are considered to have high-support needs autism, those with most severe manifestation of the condition. That would equal about 0.8 percent of all US children — which would be a fairly marginal increase from autism rates 30 years ago. Or look at it another way: In 2000, as many as 60 percent of the people being diagnosed with autism had an intellectual disability, one of the best indicators of high-support needs autism. In 2022, that percentage was less than 40 percent.

As a recently published CDC report on autism prevalence among young children concluded, the increase in autism rates can largely be accounted for by stronger surveillance and more awareness among providers and parents, rather than a novel toxin or some other external factor driving an increase in cases.

Other known risk factors — like more people now having babies later in their life, given that parental age is linked to a higher likelihood of autism — are more likely to be a factor than anything Kennedy is pointing at, experts say.

“It’s very clear it’s not going to be one environmental toxin,” said Alison Singer, founder of the Autism Science Foundation and parent of a child with profound autism. “If there were a smoking gun, I think they would have found it.”

The “dead end” that’s actually given us a clearer understanding of autism’s complexity

While Kennedy has fixated on vaccines and environmental influences, scientists have gained more precision in mapping human genetics and identifying the biological mechanisms that appear to be a primary cause of autism. And that not only helps us understand why autism develops, but potentially puts long-elusive therapies within reach.

It began with an accident in the 1990s.

Stephen Scherer, now director of the Center for Applied Genomics at the Hospital for Sick Children in Toronto, began his career in the late 1980s trying to identify the gene that caused cystic fibrosis — in collaboration with Francis Collins, who went on to lead the Human Genome Project that successfully sequenced all of the DNA in the human genome in the early 2000s. Scherer and Collins’s teams focused on chromosome 7, identified as a likely target by the primitive genetic research available at the time, a coincidence that would reorient Scherer’s career just a few years later, putting him on the trail of autism’s genetic roots.

After four years, the researchers concluded that one gene within chromosome 7 caused cystic fibrosis. Soon after Scherer helped crack the code on cystic fibrosis, in the mid-1990s, two parents from California called him: He was the world’s leading expert on chromosome 7, and recent tests had revealed that their children with autism had a problem within that particular chromosome.

That very same week, Scherer says, he read the findings of a study by a group at Oxford University, which had looked at the chromosomes of families with two or more kids with autism. They, too, had identified problems within chromosome 7.

“So I said, ‘Okay, we’re going to work on autism,’” Scherer told me. He helped coordinate a global research project, uniting his Canadian lab with the Oxford team and groups in the US to run a database that became the Autism Genome Project, still the world’s largest repository of genetic information of people with autism.

They had a starting point — one chromosome — but a given chromosome contains hundreds of genes. And humans have, of course, 45 other chromosomes, any of which conceivably might play a role. So over the years, they collected DNA samples from thousands upon thousands of people with autism, sequenced their genes, and then searched for patterns. If the same gene is mutated or missing across a high percentage of autistic people, it goes on the list as potentially associated with the condition.

Scientists discovered that autism has not one genetic factor, but many — further evidence that this is a condition of complex origin, in which multiple variables likely play a role in its development, rather than one caused by a single genetic error like sickle-cell anemia.

Here is one way to think about how far we have come: Joseph Buxbaum, the director of the Seaver Autism Center for Research and Treatment at the Icahn School of Medicine at Mount Sinai in New York, entered autism genetics research 35 years ago. He recalls scientists being hopeful that they might identify a half dozen or so genes linked to autism.

They have now found 500 genes — and Buxbaum told me he believed they might find a thousand before they are through. These genetic factors continue to prove their value in predicting the onset of autism: Scherer pointed to one recent study in which the researchers identified people who all shared a mutation in the SHANK3 gene, one of the first to be associated with autism, but who were otherwise unalike: They were not related and came from different demographic backgrounds. Nevertheless, they had all been diagnosed with autism.

Precisely how much genetics contributes to the development of autism remains the subject of ongoing study. By analyzing millions of children with autism and their parents for patterns in diagnoses, multiple studies have attributed about 80 percent of a person’s risk of developing autism to their inherited genetic factors.

But of course 80 percent is not 100 percent. We don’t yet have the full picture of how or why autism develops. Among identical twins, for example, studies have found that in most cases, if one twin has high-support needs autism, the other does as well, affirming the genetic effect. But there are consistently a small minority of cases — 5 and 10 percent of twin pairs, Scherer told me — in which one twin has relatively low-support needs while the one requires a a high degree of support for their autism.

Kennedy is not wholly incorrect to look at environmental factors — researchers theorize that autism may be the result of a complex interaction between a person’s genetics and something they experience in utero.

Scientists in autism research are exploring the possible influence when, for example, a person’s mother develops maternal diabetes, high blood sugar that persists throughout pregnancy. And yet even if these other factors do play some role, the researchers I spoke to agree that genetics is, based on what we know now, far and away the most important driver.

“We need to figure out how other types of genetics and also environmental factors affect autism’s development,” Scherer said. “There could be environmental changes…involved in some people, but it’s going to be based on their genetics and the pathways that lead them to be susceptible.”

While the precise contours of Health Department’s new autism research project is still taking shape, Kennedy has that researchers at the National Institutes of Health will collect data from federal programs such as Medicare and Medicaid and somehow use that information to identify possible environmental exposures that lead to autism. He initially pledged results by September, a timeline that, as outside experts pointed out, may be too fast to allow for a thorough and thoughtful review of the research literature. Kennedy has since backed off on that deadline, promising some initial findings in the fall but with more to come next year.

RFK Jr.’s autism commission research risks the accessibility of groundbreaking autism treatments

If Kennedy were serious about moving autism science forward, he would be talking more about genetics, not dismissing them. That’s because genetics is where all of the exciting drug development is currently happening.

A biotech firm called Jaguar Gene Therapy has received FDA approval to conduct the first clinical trial of a gene therapy for autism, focused on SHANK3. The treatment, developed in part by one of Buxbaum’s colleagues, is a one-time injection that would replace a mutated or missing SHANK3 gene with a functional one. The hope is that the therapy would improve speech and other symptoms among people with high-needs autism who have also been diagnosed with a rare chromosomal deletion disorder called Phelan-McDermid syndrome; many people with this condition also have Autism spectrum disorder.

The trial will begin this year with a few infant patients, 2 years old and younger, who have been diagnosed with autism. Jaguar eventually aims to test the therapy on adults over 18 with autism in the future. Patients are supposed to start enrolling this year in the trial, which is focused on first establishing the treatment’s safety; if it proves safe, another round of trials would start to rigorously evaluate its effectiveness.

“This is the stuff that three or four years ago sounded like science fiction,” Singer said. “The conversation has really changed from Is this possible? to What are the best methods to do it? And that’s based on genetics.”

Researchers at Mount Sinai have also experimented with delivering lithium to patients and seeing if it improves their SHANK3 function. Other gene therapies targeting other genes are in earlier stages of development. Some investigators are experimenting with CRISPR technology, the revolutionary new platform for gene editing, to target the problematic genes that correspond to the onset of autism.

But these scientists fear that their work could be slowed by Kennedy’s insistence on hunting for environmental toxins, if federal dollars are instead shifted into his new project. They are already trying to subsist amid deep budget cuts across the many funding streams that support the institutions where they work.

“Now we have this massive disruption where instead of doing really key experiments, people are worrying about paying their bills and laying off their staff and things,” Scherer said. “It’s horrible.”

For the families of people with high-needs autism, Kennedy’s crusade has stirred conflicting emotions. Alison Singer, the leader of the Autism Science Foundation, is also the parent of a child with profound autism. When I spoke with her, I was struck by the bind that Kennedy’s rhetoric has put people like her and her family in.

Singer told me profound autism has not received enough federal support in the past, as more emphasis was placed on individuals who have low support needs included in the expanding definitions of the disorder, and so she appreciates Kennedy giving voice to those families. She believes that he is sincerely empathetic toward their predicament and their feeling that the mainstream discussion about autism has for too long ignored their experiences in favor of patients with lower support needs. But she worries that his obsession with environmental factors will stymie the research that could yield breakthroughs for people like her child.

“He feels for those families and genuinely wants to help them,” Singer said. “The problem is he is a data denier. You can’t be so entrenched in your beliefs that you can’t see the data right in front of you. That’s not science.”