Exclusive: Inside the CDC Exodus and RFK Jr.’s Anti-Vaccine Crusade

As head of the U.S. Department of Health and Human Services (HHS), Robert F. Kennedy Jr. has promised to lead with “radical transparency,” follow “gold-standard science,” and maintain vaccine access. But top officials at the U.S. Centers for Disease Control and Prevention (CDC) tell TIME that Kennedy has done only the opposite—prompting them to resign in late August from the agency. Their accounts include previously unreported details about the turmoil unfolding at one of the nation’s leading health agencies.

Kennedy has repeatedly sidelined CDC officials, ignored established research, circumvented scientific protocols, and pushed a vaccine agenda rooted in ideology and not science, say Dr. Debra Houry, CDC’s former chief medical officer; Dr. Demetre Daskalakis, the agency’s ex-vaccine chief; and Dr. Daniel Jernigan, who led the department that oversees vaccine safety.

Kennedy has stacked a key vaccine-advisory committee with vaccine opponents and granted special status to a vaccine skeptic allowing him unhampered access to part of a sensitive CDC vaccine database, they say. His office has, without explanation, held up a data project that CDC scientists say would make the agency’s data more transparent. And he has made major policy decisions, including changing vaccine recommendations, without consulting top CDC scientists, the former officials say. 

Houry, Daskalakis, and Jernigan resigned on Aug. 27, the same day the White House fired CDC Director Susan Monarez. Jennifer Layden, another top CDC official, also resigned. The four former officials spoke to TIME this week.

“You get to the point where if you stay, you’re complicit,” Daskalakis says. “I couldn’t just sit there and not say this is horribly wrong.” In his resignation letter, the former director of the National Center for Immunization and Respiratory Diseases wrote that he could no longer serve “in an environment that treats CDC as a tool to generate policies and materials that do not reflect scientific reality and are designed to hurt rather than to improve the public’s health.”

Monarez wrote in an op-ed published in the Wall Street Journal on Sept. 4 that she was instructed by Kennedy in a recent meeting to rubber-stamp all recommendations from the Advisory Committee on Immunization Practices (ACIP), an independent group that is supposed to advise the CDC director on vaccines, even though the director isn’t required to accept its recommendations. In an unprecedented move, Kennedy fired all ACIP members in June and replaced them with his allies, including several vaccine opponents. 

Monarez wrote that she was fired because she refused to compromise science.

“I hit my line when it became clear that Susan was being totally sidelined on the topic of vaccines,” Daskalakis says. “ACIP is being led by ideologues that don’t have regard for science. I know how this story ends. It will limit the ability of people to get vaccines.” 

Kennedy defended the CDC shakeup during a Senate Finance Committee hearing on Sept. 4, saying that the changes were necessary to “restore the agency to its role as the world’s gold-standard public health agency.” He said Monarez lied about the factors that had led to her firing and that he didn’t have a private meeting with her.

HHS did not respond to TIME’s request for comment.

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Monarez had earlier tried to appoint a new designated federal official for ACIP, but had been blocked by Kennedy’s office, Houry says. The official attends committee meetings and ensures members are complying with federal law and the correct protocols. Monarez had wanted to appoint someone with more legal and policy experience to the role given the inexperience of most current ACIP members, Houry says. “The final straw for me was when Susan couldn’t make that change. Any hope I had in scientific integrity was gone.”

At its first meeting in June, the new ACIP committee heard a presentation on the risks of thimerosal, a preservative that anti-vaccine activists have claimed is linked to autism. CDC scientists prepared a document for the meeting that showed, based on multiple studies, no link between thimerosal in vaccines to autism or other neurodevelopmental disorders. (For more than two decades, thimerosal has not been used in childhood vaccines except for flu vaccines in multi-dose vials. Most flu vaccines in the U.S. are given in single-dose vials that don’t contain thimerosal.) The document was initially posted online but was taken down on the day of the meeting at the behest of Kennedy’s office, Daskalakis says.

“They were cherrypicking what they wanted the American public to see,” he says. 

ACIP recommended that thimerosal be removed from all vaccines. HHS said in July that it was adopting the committee’s recommendation.

One of the key roles of the CDC is to provide scientific data and analyses to the Health Secretary and others, including ACIP, to help guide public-health policy and recommendations. But Daskalakis, Houry, and Jernigan say Kennedy barely engaged with CDC staff and disregarded CDC data that was provided, particularly related to vaccines. 

Daskalakis and Houry say they offered to brief Kennedy on a variety of public-health issues but were never invited to do so. Jernigan, former director of the National Center for Emerging and Zoonotic Infectious Diseases, says members of his staff were invited to a single scientific meeting with Kennedy, which took place in August and focused on Lyme disease. Jernigan says HHS staff told his team to avoid discussing the Lyme disease vaccine, which is under development for people.

Jernigan, Houry, and Daskalakis say they were in a meeting in May with other top CDC officials when they learned, via the social-media platform X, that Kennedy had announced a change to the CDC’s recommended vaccine schedules. 

“Radical transparency? Well, that’s not how you want to find out about COVID vaccine guidance,” Houry says. 

Layden, a fourth CDC official who resigned last week, said she left the agency because recent budget and staffing cuts, coupled with a lack of leadership support, had made it impossible for her to do her job. Layden was the director of CDC’s Office of Public Health Data, Surveillance and Technology, which oversees the agency’s data-modernization efforts. She says her group had recently completed a new website that centralizes data of all reportable infectious diseases. The CDC currently has separate websites for each disease, which can be hard to navigate.

“The idea was to create a one-stop shop,” Layden says. 

But Kennedy’s office needs to greenlight the website before it can be made public. “We never got the approval to release it,” Layden says. “No reasoning has been given.” 

Not publishing a website that provides clearer data is “inconsistent with being transparent,” she says.

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As of last week, no one at CDC had seen the agenda for the next ACIP meeting, scheduled to take place later this month, Daskalakis says. CDC scientists are usually involved months ahead of such meetings and provide guidance and data to the committee.

The agenda has since been posted online and lists respiratory syncytial virus (RSV) as one of the issues up for discussion. “No one at CDC has any idea what that topic is about,” Daskalakis says.

CDC staff are also in the dark about what David Geier, a longtime vaccine opponent who Kennedy tapped earlier this year to conduct vaccine-safety research, is up to, says Jernigan.

Kennedy has granted Geier special access to part of the CDC’s Vaccine Safety Datalink (VSD), Jernigan says. Scientists use the VSD to monitor vaccine safety and conduct studies about adverse events following vaccination. 

The VSD is a collaboration between the CDC and about a dozen large health care networks. The CDC only owns VSD data collected before 2000, and that is the data Geier has been given access to, Jernigan says. Unlike other researchers, however, Geier hasn’t been required to provide information to the CDC about what he is using the data for or explain what steps he is taking to protect the private health information contained in the VSD, the former official says. 

“We asked him to present a study question and protocol. We have never seen those documents,” Jernigan says. “That’s not transparent. That’s not gold-standard science.” 

Geier is expected to produce a report based on his research soon, Jernigan says. 

Geier, whose highest credential is a bachelor’s degree in biology, has built his career attempting to show a link between vaccines and autism. Large studies conducted over decades have shown no such link. 

In the 2000s, Geier, together with his late father and collaborator, Mark Geier, were barred from accessing the VSD at least twice by CDC officials who said they had misused it. Jernigan says he had misgivings about providing VSD access to Geier, but was told by an HHS attorney that Geier had been designated as a direct agent of Kennedy’s. “Our engagement with David was equivalent to engaging with” Kennedy himself, Jernigan says.

Jernigan, Houry, and Daskalakis say that Kennedy’s vaccine moves are already harming Americans. After changes to federal COVID-19 vaccine guidance were announced, CVS and Walgreens said last week they would restrict access to COVID-19 shots in several states.