UPDATE (October 11, 2025, 8:46 p.m. ET): This piece has been updated because, following publication, many fired employees began receiving emails communicating that despite the earlier notice, they would no longer be terminated.

Health Secretary Robert F. Kennedy Jr. moved one step closer to his goal of dismantling the nation’s premier public-health agency by dismissing more than 1,000 scientists, doctors and public health officials from the Department of Health and Human Services late Friday night.

The dramatic move came during the second week of a government shutdown and is part of the Trump administration’s aggressive push to even further slash the size of the federal workforce and punish Democrats. The culling reportedly started with at least 4,000 people across departments including Education, Treasury, Housing and Urban Development and Energy, among others.

But the bloodshed at the Centers for Disease Control and Prevention was especially acute, according to a list crowdsourced by CDC employees who received layoff notices that was viewed by BLN. The firings ran across more than a dozen CDC divisions and centers, wiping out entire offices and teams that investigate disease outbreaks, manage infectious disease responses, collect data, publish scientific reports and communicate with global partners and Congress.

“CDC is over. It was killed,” said Dr. Demetre Daskalakis, the former director of the CDC’s National Center on Immunization and Respiratory Diseases, who recently resigned to protest what he described as Kennedy’s unscientific takeover of the CDC. “This administration only knows how to break things. They have made America at risk for outbreaks and attacks by nefarious players. People should be scared.”

BLN spoke with eight current and former CDC officials, most of whom requested anonymity for fear of retaliation against themselves or their remaining colleagues.

The emails alerting staffers came late Friday night, but current and former employees said CDC staffers had been bracing for layoffs since President Donald Trump signaled that he would use mass reductions in force as a way to punish Democrats for the ongoing shutdown, caused by a budget standoff between Republicans and Democrats.

Notification that they’d lost their jobs came even as the human resources professional tasked with implementation had been furloughed as part of the shutdown.

Several current and former officials said they initially believed the cuts — like other chaotic firings that were later walked back — might not be permanent. And there is a question about the legality of all employee firings during the shutdown. And, indeed, following publication of this article, many fired employees began receiving emails with the subject line, “Recession of Previous Notice of Reduction in Force,” communicating that that despite the earlier notice, they would no longer be fired. An HHS official who declined to be named because he was not approved to speak on the issue, told BLN that around half of the firings had been done in error.

The official said leadership in the Immunization and Respiratory Diseases Center, the Global Health Center, the Morbidity and Mortality Weekly Report team, the Epidemic Intelligence Service, and scientists working on responses to outbreaks of Ebola in the Democratic Republic of Congo and measles in the U.S., had received or would soon receive notices that their lay-offs had been rescinded. The official said the accidental firings had been the result of a “miscoding error.”

Regardless, three senior officials said, the damage has already been done.

In a move that may alarm lawmakers, the CDC’s entire Washington office was also cut. That office served as the agency’s conduit to Congress and to the broader Washington, D.C., public health community.

HHS spokesperson Andrew Nixon texted a statement that blamed Democrats for the sweeping cuts and called the public health agency “a bloated bureaucracy.”

The incident manager and the deputy incident manager tasked with measles response were also fired, according to three senior sources. Both are being reinstated, however, according to a senior official. The country is experiencing its largest measles outbreak in three decades. Three people have died of measles this year and hundreds of children are currently forced to quarantine because of outbreaks in South Carolina and Minnesota.

“All HHS employees receiving reduction-in-force notices were designated non-essential by their respective divisions. HHS continues to close wasteful and duplicative entities, including those that are at odds with the Trump administration’s Make America Healthy Again agenda,” Nixon’s statement said.

The CDC has traditionally operated as a nonpartisan institution — its career officials have served under both Republican and Democratic administrations. But there has been a sharp departure from that norm under Kennedy’s tenure.

Trump warned he would seek to ensure the harshest effects of the shutdown would affect Democratic priorities.

“We’re only cutting Democrat programs,” Trump said Thursday during a Cabinet meeting.

The current sweep of the governmentwide cuts is still unknown, but seems to target leadership positions, according to two former senior officials. A former senior official said the CDC cuts amounted to more than 9% of the agency’s remaining workforce, which had already weathered mass layoffs early this year.

A former senior official said the CDC cuts amounted to more than 9% of its remaining workforce, which had already weathered mass layoffs early this year.

The entire director’s office at the National Center for Immunization and Respiratory Diseases — meaning all the center’s leaders — was wiped out, a deletion that would likely disrupt critical public health functions at home and abroad.

Similarly, the office of the director at the CDC’s Global Health Center was abolished. That center is tasked with tracking and responding to health threats globally. Its goal — in addition to saving lives in other countries — is to “stop health threats at their source before they spread to the United States.”

The cuts also included the team that publishes the Morbidity and Mortality Weekly Report, the agency’s flagship journal that had been publishing fewer articles since Kennedy took over. (As of Saturday night, all those offices were being reinstated, according to the HHS official.)

One current CDC official said it “means not only is he silencing CDC, he can prevent states and anyone else in the field from using the best tool they have for sharing their own science.”

The Epidemic Intelligence Service and the Laboratory Leadership Service were also gutted. Those programswhich track global outbreaks, are staffed by a group known to become the next generation of scientists and public health leaders. (That office, too, is being reinstated, according to the HHS official.)

“These cuts have consequences,” said Dr. Deb Houry, the former CDC deputy director and chief medical officer who resigned in protest in August. “I am concerned about the safety of the American public.”

The cuts ripped through the center that forecasts diseases and responds to public health emergencies and the center that tracks and implements prevention programs for injuries from suicide to overdoses.

“Capacity to respond to things like suicide clusters in communities has been decimated,” Houry said.

Kennedy’s tenure at HHS has been unprecedented and chaotic. In just eight months, the secretary has: pushed sweeping budget cuts and canceled billions in research and development; overseen mass layoffs and reorganizations that erased whole teams tackling clear health threats; without scientific backing, withdrawn Covid vaccine recommendations for healthy children and pregnant people; gutted the agency’s vaccine advisory panel, firing respected experts and replacing them with ideological loyalists; installed a vocal Covid vaccine critic to chair a safety subcommittee; reopened the long-debunked vaccines-and-autism debate; hired a discredited anti-vaccine researcher who experimented on autistic children to trawl government data and relitigate settled science; pressed for access to private data to fuel the research; undermined his own epidemiologists during the Texas measles response; downplayed a shooting that left CDC staff shaken; announced sweeping policy changes on social media with no data to back them and accused the American Academy of Pediatrics of a “pay-to-play scheme” for daring to dissent. Most recently, he blew his self-imposed September deadline to figure out the cause of autism and, without compelling scientific evidence, blamed pregnant mothers’ use of Tylenol for the condition.

At the same time, a horde of experienced officials have quit or been pushed out and replaced with anti-vaccine allies and loyalists lacking public health experience or scientific credentials.

Firing so m any CDC leaders is in line with Kennedy’s pattern of forcing out career scientists and experts in key positions. That has left offices unfilled and resulted in him being surrounded by staffers willing to rubber-stamp his unscientific directives.

In Septemberrecently ousted CDC Director Susan Monarez, testified to senators on the Senate Health, Education, Labor and Pensions Committee that Kennedy had personally ordered her to fire center directors and “promote the next group, and continue to do so until I got to an organization that was compliant” with his demands. Kennedy has said he fired Monarez because she was “not a trustworthy person.”

Kennedy has vilified the CDC for two decades. In videos from anti-vaccine conferences, he likened the agency’s vaccine work to “fascism” and “child abuse,” calling it a “cesspool of corruption” full of scientists who were hiding the alleged link between autism and vaccines.

In a 2023 interview during his failed presidential run, Kennedy said of the CDC and other public health agencies that he wanted to “unravel the corrupt corporate capture of these agencies that turned them predatory, against the American public.” He said he planned to fire officials in charge and appoint people who would “turn them back into healing and public health agencies.”

Neither Kennedy nor the CDC’s acting director, Jim O’Neill — a recent political appointee with little experience — had commented publicly on the firings by Saturday afternoon. O’Neill’s most recent post to X was a photo of what he said was a bald eagle flying over the Capitol, taken from his Washington, D.C., office. He captioned it, “Good morning we are going to win.”

Brandy Zadrozny

Brandy Zadrozny is a senior enterprise reporter for BLN. She was a previously a senior enterprise reporter for NBC News, based in New York.