Less than 24 hours after Robert F. Kennedy Jr. became the nation’s health secretary, his press secretary delivered an order from him to the Centers for Disease Control and Prevention: Take down your advertising campaign promoting flu vaccines.
It was Feb. 14, 2025. Flu season was in full swing and it was a bad one. That same day, the C.D.C. reported that influenza-related ailments had killed 68 children — 11 that week alone — and 16,000 people overall. There had been 29 million reported cases and 370,000 hospitalizations.
Nicole Coffin, the veteran communications expert who took the press secretary’s call, dashed off an email to her supervisor, Kevin Griffis. “Andrew Nixon/HHS gave me a call and asked that we pull out of circulation all campaign ad buys related to flu or anything encouraging shots or vaccinations,” she wrote, referring to the Health and Human Services Department, which Mr. Kennedy leads. “He said this request came directly from the Secretary.”
Alarmed, Mr. Griffis wrote to his boss, Susan Monarez, the acting C.D.C. director, warning that halting the campaign in the middle of an outbreak “presents significant reputational risk to the agency” and could raise “legal issues.”
The exchanges over the flu vaccine campaign are in a cache of internal C.D.C. emails obtained last week by The New York Times, and published online on Monday. The messages provide a detailed look at a period of transition in which the leaders of the nation’s public health agency frequently found themselves buffeted and dismayed by the agenda imposed by Mr. Kennedy and the new Trump administration.
The emails begin in January, before Mr. Kennedy was confirmed, and end in mid-August, about a week before the White House fired Dr. Monarez as C.D.C. director at the secretary’s request, just 29 days after her Senate confirmation. While Mr. Kennedy’s fraught relationship with the health agency is well known, the messages, coupled with interviews, shed light on how C.D.C. employees scrambled to meet his demands — often on matters regarding vaccines and autism — as the administration gutted the agency’s ranks.
When Mr. Kennedy was considering remaking the Advisory Committee for Immunization Practices, the panel of outside experts that advises the C.D.C. on vaccine policy, agency employees were dispatched to a nearby National Archives facility to dig up 60 years’ worth of historical information on the committee, including its original charter from 1964 and policies on how it handled conflicts of interest.
The request came from Stuart Burns, a close ally of the secretary who functions as his point man inside the C.D.C. director’s office. A staff member initially said Mr. Burns needed the information by the next day, to “inform his understanding of the current state of ACIP operations, as well as the historical glide path that brought us here.” But the research took several weeks, including a search of the C.D.C.’s museum and a trip to the archives in Morrow, Ga., about a 40-minute drive from the agency’s headquarters in Atlanta.
When it was over, Dr. Debra Houry, the agency’s chief medical officer at the time, wrote to Mr. Burns that it would be “helpful to prioritize,” in the future, given how many people had been laid off.
“Can we discuss?” she wrote. “Staff had to pull 28 boxes for this request.”
Dr. Houry gave more than 250 pages of emails to the Senate health committee in response to its written questions after she testified in September. She was a party to all the messages. A former emergency physician who worked at the C.D.C. under three presidents, she said in an interview that she wanted to “shine the light” on public health decisions she considered dangerous.
The panel’s ranking member, Senator Bernie Sanders, independent of Vermont, posted the emails on Monday evening along with a memo from his staff. A spokesman for the committee chairman, Senator Bill Cassidy, Republican of Louisiana, did not respond to a request for comment on what the panel might do with them.
Officials at the Department of Health and Human Services did not respond to a detailed list of questions about the emails. But Mr. Kennedy has said repeatedly that he regards the C.D.C. as corrupt, and that he feels an obligation as secretary to shake things up, both in the agency and in his department, including by firing people.
“I came into this job to change the culture of a broken agency that has presided over the worst decline in public health in American history,” he recently wrote on X, in a post criticizing coverage by The Times of his management of the health department.
Testifying on Capitol Hill after he fired Dr. Monarez as head of the agency, the secretary told senators that “effectiveness — not politics — will be the watchword of our leadership.” But the emails confirm Dr. Monarez’s own Senate testimony that President Trump’s political appointees were firmly in control.
“Susan,” wrote Matthew Buckham, then Mr. Kennedy’s chief of staff, on Aug. 19. “Let’s get on a call this week to discuss in depth, but until we can connect directly, I wanted to elevate the absolute need for political review of major policy decisions at CDC.”
The aim, he wrote, was to ensure that “political leadership all have eyes” on major decisions and that personnel changes needed to be run past the White House.
“We will talk soon,” Mr. Buckham concluded, signing the message, “Make America Great! Matt.”
The pressure from Mr. Kennedy’s aides in Washington, who took office before he was confirmed, began before his arrival, the emails show. President Trump’s executive order, issued on his first day in office, “ending radical and wasteful government D.E.I. programs” prompted C.D.C. officials to remove hundreds of agency web pages, including data.cdc.gov — a massive collection of public health data — that might contain information about race or gender.
But at 10:30 p.m on Friday, Jan. 31 — one day after Mr. Kennedy wrapped up his Senate confirmation hearings — Dr. Monarez issued an urgent plea.
“Apologies for the late request, but we need to get the ACIP website up and functioning,” she wrote referring to the panel of vaccine advisers. Noting that some web pages were no longer functioning “likely due to language modifications needing to be implemented,” she asked her underlings to call her as soon as they got the message, so they could talk about an “expedited process.”
The emails did not offer a reason. But Dr. Houry, and another former employee who spoke on condition of anonymity to avoid a backlash, said in interviews that Mr. Kennedy’s aides, already at work in Washington, feared that removing vaccine-related pages might endanger Mr. Kennedy’s chances of being confirmed.
At 8:30 the following morning, C.D.C. leaders had a telephone negotiating session with top health department leaders, including Stefanie Spear, Mr. Kennedy’s closest adviser and later his deputy chief of staff, to figure out what would stay and what would go. They devised a color-coded spreadsheet: green for pages that had gone back up; red for pages that needed to stay down; yellow for pages that “HHS” — shorthand for Mr. Kennedy’s office — wanted restored.
The advisory committee pages were put back up, with the exception of information about vaccines to prevent mpox, a sexually transmitted disease that primarily affects men who have sex with men. The mpox website has since been restored, although the C.D.C. has reverted to calling the disease “monkeypox,” a name that the World Health Organization abandoned in 2022 after agreeing with public health experts who said it was racist and stigmatized patients.
C.D.C. political leaders went to great lengths to install Mr. Kennedy’s allies in key positions, even if they did not have crucial professional qualifications for the job, the documents show. The agency tried to use Title 42, a federal code that permits scientific experts to be hired without going through the regular civil service process, to put a businessman who was a longtime activist on behalf of parents of children with autism in charge of its National Center on Birth Defects and Developmental Disabilities.
The activist, Mark Blaxill, a Harvard Business School graduate and founder of the group SafeMinds, has written books and medical journal articles on autism; one was retracted in 2023. C.D.C. human resources officials concluded that he lacked the scientific qualifications to be considered a “distinguished consultant” under the law. He now works at the agency in another capacity, and does not run the birth defects center.
The emails confirm, as The Times has previously reported, that Mr. Kennedy was deeply involved in efforts to gain control over the Vaccine Safety Datalink, or VSD, a database of millions of confidential medical records that, he believes, has the potential to prove a link between vaccines and autism, a theory that has been debunked in numerous studies. His own top aides were under pressure, too.
Mr. Kennedy “wants to buy all the VSD data and put it in the office of the Secretary,” Reyn Archer, his senior counselor, wrote to Dr. Houry and other officials. “This may be a leap but there are other ways to achieve this but today CDC is not ready to take big leaps. I am being told we must find a way to take big leaps. I need your help on this.”
While the secretary steered clear of most career scientists, at least in his early days in office, he was giving direct instructions to one of them, William Thompson, who has challenged a 2004 C.D.C. study that concluded the measles vaccine was not linked to autism, and works under government whistle-blower protections.
Dr. Thompson was working to compile data sources for future autism studies; he called it a “high priority for Secretary Kennedy.” A note from the secretary appears just once in the email collection. He weighed in with a one-sentence message during a conversation with Dr. Thompson about a two-decade old data set used by a former C.D.C. researcher, Thomas Verstraeten.
“Bill. I’m assuming this is the verstratten original data,” Mr. Kennedy wrote.
In interviews, former employees said they wrote their emails with history in mind; they wanted to document what was happening. By and large, the notes are polite exchanges between colleagues who are trying to get along under difficult circumstances. But Dr. Houry sometimes sounded exasperated, as when Mr. Burns asked for 10 years’ worth of measles data while C.D.C. “disease detectives” were being deployed to Texas to fight the outbreak.
“Let me see how much work it will take team,” Dr. Houry replied, clearly writing in a hurry. “The active measles response has to take priority.”
