Robert F. Kennedy Jr., President-elect Donald Trump’s choice to lead the nation’s health agencies, formally asked the Food and Drug Administration to revoke the authorization of all COVID-19 vaccines during a deadly phase of the pandemic when thousands of Americans were still dying every week.

Kennedy filed a petition with the FDA in May 2021 demanding that officials rescind authorization for the shots and refrain from approving any COVID vaccine in the future.

Just six months earlier, Trump had declared the COVID vaccines a miracle. At the time that Kennedy filed the petition, half of American adults were receiving their shots. Schools were reopening and churches were filling.Estimates had begun to show that the rapid rollout of COVID vaccines had already saved about 140,000 lives in the United States.

The petition was filed on behalf of the nonprofit that Kennedy founded and led, Children’s Health Defense. It claimed that the risks of the vaccines outweighed the benefits and that the vaccines weren’t necessary because good treatments were available, including ivermectin and hydroxychloroquine, which had already been deemed ineffective against the virus.

The petition received little notice when it was filed. Kennedy was then on the fringes of the public health establishment, and the agency denied it within months. Public health experts told about the filing said it was shocking.

John Moore, a professor of immunology at Weill Cornell Medical College, called Kennedy’s request to the FDA “an appalling error of judgment.” Gregg Gonsalves, an epidemiologist at the Yale School of Public Health, likened having Kennedy lead the federal health agencies to “putting a flat earther in charge of NASA.”

Dr. Robert Califf, commissioner of the FDA, described Kennedy’s effort to halt the use of COVID vaccines as a “massive error.”

Kennedy’s transition spokesperson did not respond to requests for comment, but has said recently that he does not want to take vaccines away.

Asked in November by an NBC reporter about his general opposition to COVID vaccines — and whether he would have stopped authorization — Kennedy said he was concerned that the vaccines did not prevent transmission of the virus.

“I wouldn’t have directly blocked it,” he said. “I would have made sure that we had the best science, and there was no effort to do that at that time.”

Kennedy’s early opposition to COVID vaccines has alarmed public health experts, many of whom contend that it should disqualify him from overseeing health agencies with the power to authorize, monitor and allocate funding for millions of vaccines each year.

They are also concerned about how he might handle a possible bird flu pandemic, which could necessitate a rapid deployment of vaccines.

As Kennedy prepares for his confirmation hearings before two Senate committees, he and his allies have insisted that he is not anti-vaccine.

In fact, in mid-2023, he told a House panel that he had taken all recommended vaccines — except for the COVID immunization.

At his confirmation hearings, he’ll most likely face scrutiny of his broader statements on vaccines, including that the polio vaccine cost more lives than it saved.

Trump has stepped forward in recent weeks to defend Kennedy after The New York Times reported that one of Kennedy’s lawyers had previously petitioned the FDA to revoke approval or pause distribution of several polio vaccines over safety concerns.

“I think he’s going to be much less radical than you would think,” Trump said last month.

After the Times report, Trump and Kennedy expressed their support for the polio vaccine.

If confirmed by the Senate as secretary of the Health and Human Services Department, Kennedy would assume oversight of $8 billion in funding for the Vaccines for Children program and would have the authority to appoint new members to a panel that makes influential vaccine recommendations to states.

At the time that Kennedy challenged the COVID vaccines, some of his objections touched on wider concerns about their rapid development. Emergency-use authorization — a preliminary form of approval — for immunizations was unusual. Others argued that a public health emergency dictated a speedier rollout.

Dr. Jennifer Nuzzo, director of the Pandemic Center at Brown University School of Public Health, said it would be reasonable to debate whether COVID vaccines should have been subject to additional study.

But she profoundly disagreed with Kennedy’s views, saying that “the idea that in early 2021 that you could be saying that people over the age of 65 don’t need COVID vaccines — that’s just nuts.”

Vaccines have rare side effects, and there have been cases of injury from the COVID shots. Government officials weigh the harms against the potential to save lives. An estimate released in early 2024 found that the COVID vaccines and mitigation measures saved about 800,000 lives in the United States.

Another study found that in late 2021 and 2022, COVID death rates among unvaccinated people were 14 times the rates of those who had received a COVID booster shot. Researchers also estimated that from May 2021 through September 2022, more than 230,000 deaths could have been prevented among people who declined initial COVID inoculations.

From the start of the COVID vaccine campaign, Kennedy’s view that the COVID vaccines were dangerous put him at odds with Trump, whose Operation Warp Speed to develop the vaccines was one of his policy triumphs. And Kennedy went on a concerted campaign against the vaccine.

Kennedy told Louisiana lawmakers in late 2021 that the COVID vaccine was the “deadliest vaccine ever made.”