A steadfast figure in the anti-vaccine movement who has helped shape Health Secretary Robert F. Kennedy Jr.’s thinking on a possible link to autism has joined his department to work on a study examining the long-debunked theory, according to people familiar with the matter.

The new analyst, David Geier, has published numerous articles in the medical literature attempting to tie mercury in vaccines to autism. In 2012, state authorities in Maryland found that he had been practicing medicine without a license alongside his father, Mark Geier, who was a doctor at the time.

Maryland authorities also suspended Mark Geier’s medical license following claims that he endangered children with autism and exploited their parents, according to state records.

Federal judges have rejected their research on autism and vaccines as too unreliable to stand up in court.

David Geier’s new government role has stunned public health experts, who had already expressed concerns about Mr. Kennedy’s decisions to cancel a long-held vaccine meeting and to cut grants focused on understanding vaccine hesitancy.

In addition, David Geier’s involvement in government research heightens their fears that vaccine confidence could be further eroded, especially after Mr. Kennedy’s recent embrace of questionable alternative treatments for measles during the sprawling outbreak in Texas.

“If we increase vaccine hesitancy and immunization rates go down further, we will see more vaccine-preventable disease outbreaks,” said Dr. Christopher Beyrer, director of the Duke Global Health Institute. “That’s how it works.”

Several experts said that appointing David Geier to work on a study of vaccine safety preordains the outcome — like having a basketball referee show up in one team’s jersey.

“You’d think you’d want a fresh eye,” said Edward L. Hunter, a former head of the Washington office of the Centers for Disease Control and Prevention.

“This isn’t a fresh eye. They have already published their results, and spending all this time and money is not going to help anyone. I am quite certain they’ll come to the same conclusion.”

An official with Mr. Kennedy’s Department of Health and Human Services declined to comment. Two White House spokesmen did not respond to a request for comment. David Geier did not reply to emails or calls requesting comment.

Mary Holland, chief executive of Children’s Health Defense, the anti-vaccine nonprofit Mr. Kennedy ran until his presidential bid, praised David Geier on its website on Wednesday, describing him as “a brilliant, extremely knowledgeable researcher with deep expertise on mercury.”

(Over the weekend, federal officials ordered the nonprofit to remove a mock C.D.C. web page suggesting a link between vaccines and autism.)

David Geier is listed in the Department of Health and Human Services directory as a “senior data analyst.” News of his role in the agency was initially reported by The Washington Post.

Earlier this month, federal officials announced plans for a large study to re-examine whether there was a connection between vaccines and autism. Mr. Trump has voiced support for H.H.S. officials who wanted to revisit the issue, citing increases in autism diagnoses in children over the decades.

About 1 in 36 children have an autism diagnosis, according to C.D.C. data collected in 11 states, compared with 1 in 150 children in 2000.

Many scientists believe the rise is due in part to increased awareness of the disorder and changes in how it is diagnosed by medical professionals, though genetic and environmental factors could be playing a role as well.

The Senate confirmed Mr. Kennedy largely because he won over the chairman of the Senate health committee, Bill Cassidy, Republican of Louisiana, who is a medical doctor and strong proponent of childhood vaccines.

Mr. Cassidy has said that further research into any supposed link between vaccines and autism would be a waste of money and a distraction from studies that might shed light on the “true reason” for the rise in autism rates.

On Thursday, Mr. Cassidy said he wanted confirmation of David Geier’s role, aside from news reports. He mentioned that he had breakfast with Mr. Kennedy on Thursday but said the topic did not come up.

At one of his confirmation hearings, Mr. Kennedy shot back at Mr. Cassidy, citing a study from an ecosystem of vaccine critics that he said proved a connection between vaccines and autism.

David Geier comes from a similar circle of researchers. Along with his father, he played a formative role in Mr. Kennedy’s thinking.

Mr. Kennedy interviewed David Geier for an essay in 2005, “Tobacco Science and the Thimerosal Scandal,” in which he accused the C.D.C. of deliberately hiding vaccine data, under chapter headings like “Conspiracy” and “The Cover-Up.”

Mr. Kennedy described the Geiers’ belief that thimerosal, a mercury-containing preservative used in some vaccines, was linked to childhood autism. The preservative has since been removed from most childhood vaccines but is still used in some flu shots.

In a Rolling Stone article called “Deadly Immunity,” Mr. Kennedy credited the Geiers with being among the few who had gained access to C.D.C. vaccine data, which he said they used to “demonstrate a powerful correlation between thimerosal and neurological damage in children.” (The magazine later withdrew the article, but did not elaborate.)

Almost a decade later, in Mr. Kennedy’s book, “Thimerosal: Let The Science Speak,” he paid homage to the Geiers, mentioning them nearly 250 times. He called them a “father-and-son team of independent medical researchers” who had “published extensively on the topic of thimerosal and its potential link to neurodevelopmental disorders, particularly autism.”

Mr. Kennedy acknowledged that the two had become “lightning rods of controversy in the vaccine safety debate.”

“The Geiers have published no fewer than thirteen epidemiological studies of the associations between Thimerosal and health effects in U.S. populations, employing accepted statistical practices,” Mr. Kennedy wrote in the book.

On a podcast in 2022, Mr. Kennedy credited the Geiers’ research for showing that vaccines “had nothing to do with” a decline in infectious diseases over decades. “It was all an illusion,” Mr. Kennedy said, attributing the decrease to improving sanitation and nutrition.

The Geiers’ work has been repeatedly discredited by other scientists and federal court decisions.

An extensive review of the purported link between vaccines and autism in 2004 by the Institute of Medicine, an elite group of doctors and researchers, panned the Geiers’ studies. The review found their work to be marred by flaws “making their results uninterpretable.”

The institute’s report on a connection with the measles shots said: “The committee concludes that the evidence favor rejection of a causal relationship between M.M.R. vaccine and autism.”

In 2011, the Maryland Medical Board accused David Geier of practicing medicine without a license alongside his father at a Rockville, Md., clinic for children with autism.

One mother of a 10-year-old boy with autism balked when David Geier reportedly ordered 24 different blood tests for her son.

His father, Mark Geier, lost his medical license in 2012. Records in that case indicate that both father and son promoted a theory that thimerosal caused autism.

State authorities found that the Geiers had offered treatment with puberty-blocking drugs. To some patients, they offered chelation, a procedure to remove heavy metals from the blood, records show. David Geier was assessed a $10,000 fine.

Judges have rejected the Geiers’ efforts to serve as experts on vaccine safety in court. Records show that judges challenged the father-son team’s billings for hundreds of thousands of dollars related to services they provided as experts for a specialized vaccine injury court.

The judges cited David Geier’s lack of qualifications, which include a bachelor’s degree in biology, and raised concerns about his father’s credibility.

Judge George L. Hastings Jr. said in 2016 that David Geier was not qualified to render an expert opinion in a National Vaccine Injury Compensation court case.

Judge Hastings said his report “is neither useful nor relevant, because he is not qualified as an expert concerning the matters he discusses.”

In a review of two Geier studies this week, Jeffrey S. Morris, director of the division of biostatistics at the University of Pennsylvania, said he found what appeared to be a numerical sleight of hand that made it appear that vaccines caused a spike in autism.

“When I look at these two studies, they are so fatally flawed that I have serious concerns that any study that they’re going to design is going” to be rigorous enough, he said, “to yield valid results.”

To Mr. Hunter, formerly of the C.D.C., the decision to spend federal funds on a new study of a debunked theory would come at the cost of a meaningful discovery.

Since he became health secretary, Mr. Kennedy has presided over cutbacks involving research into nearly every aspect of health care and diseases. On Thursday, he announced a massive reorganization and reduction in the work force from 82,000 to 62,000.

“To me, the big shame is that with budget cuts, we are not ramping up research into what is actually causing autism,” Mr. Hunter said. “And if you are worried about vaccine-preventable disease, this is such a clear setback.”

Michael Gold contributed reporting from Washington. Alain Delaquérière contributed research. Jeremy Singer-Vine provided data analysis.