CDC Employees Report Turmoil Under RFK Jr. Leadership

In the fourteen months since Robert F. Kennedy Jr. took the helm at the Department of Health and Human Services, the Centers for Disease Control and Prevention has lost thousands of employees, seen its senior leadership gutted, and faces a proposed budget cut of 53 percent—all while measles cases have surged to levels not seen in over three decades. Employees describe an agency in freefall. Kennedy says he is restoring trust that the CDC squandered during the pandemic. The stakes of this dispute are measured in disease outbreaks and public health capacity.

The Workforce Exodus

The numbers tell a stark story. Since Kennedy took office, approximately 2,400 CDC employees—18 percent of the agency's workforce—have been terminated or forced into early retirement [1]. In October 2025, Kennedy dismissed more than 1,000 additional scientists, doctors, and public health officials from HHS in a single Friday night, a move employees dubbed the "Friday night massacre" [2]. Some of those firings were later reversed after courts intervened, and Kennedy himself acknowledged that HHS would need to reinstate roughly 20 percent of the reduced workforce after what he called DOGE-related "errors" [3].

The losses extended well beyond rank-and-file positions. In late August 2025, Kennedy fired CDC Director Susan Monarez just 29 days after her Senate confirmation [4]. Her offense, according to multiple accounts: she refused to pre-accept forthcoming decisions from the agency's vaccine advisory panel and declined to fire career employees without cause [5].

The firing triggered a cascade of resignations among the agency's most senior officials. Dr. Debra Houry, the CDC's deputy director and chief medical officer, resigned along with Demetre Daskalakis, director of the National Center for Immunization and Respiratory Diseases, and Dan Jernigan, director of the National Center for Emerging and Zoonotic Infectious Diseases [4]. Houry said publicly that "CDC leaders were reduced to rubber stamps, supporting policies not based in science, and putting American lives at risk" [5]. Monarez herself wrote in a Wall Street Journal op-ed that Kennedy's approach "isn't reform. It is sabotage" [6].

With the leadership vacuum, Kennedy installed his own deputy as acting CDC director [7]. By February 2026, another round of leadership changes saw HHS Deputy Secretary Jim O'Neill and General Counsel Mike Stuart depart as part of a broader pre-midterm reorganization [8].

The Budget Ax

The workforce reductions are one dimension of the contraction. The proposed FY 2026 budget would cut CDC funding by $5 billion—a 53 percent reduction compared to FY 2024 levels [9]. Over 100 public health programs and funding lines face elimination, including 61 programs at the CDC alone [9]. Among those targeted: cancer, diabetes, and heart disease prevention programs; global and domestic HIV/AIDS prevention; global immunization programs; and opioid and substance use prevention [9].

The Public Health Emergency Preparedness program—which funds state and local readiness for disease outbreaks, bioterrorism, and natural disasters—faces a 52 percent funding cut [9]. Federal agencies also terminated $12 billion in previously approved COVID-19 era grants during 2025 [9].

Source: Trust for America's Health / CDC Congressional Justification FY 2026

Data as of Mar 23, 2026CSV

According to researchers at George Washington University, approximately 42,000 jobs would be lost nationwide in 2026 if the proposed CDC budget cuts become law, with about one-third of those losses in sectors outside public health, and state and local tax revenues falling by more than $240 million [10].

In February 2026, the administration attempted to cut CDC funds that Congress had already appropriated and President Trump had signed into law, a move that was blocked by federal courts [11].

Structural Overhaul

Beyond cuts, Kennedy has pursued a sweeping organizational restructuring. Within months of taking office, he announced plans to consolidate HHS's 28 divisions into 15, creating new entities including the Administration for a Healthy America [12]. The CDC was directed to absorb the Administration for Strategic Preparedness and Response, the agency responsible for disaster and public health emergency response [12].

Entire offices were abolished. The director's office at the National Center for Immunization and Respiratory Diseases was wiped out, as was the office of the director at the CDC's Global Health Center [2]. Kennedy's vision, as described by Axios, centers on consolidating power within HHS, reducing the autonomy of individual agencies like the CDC and FDA [13].

In June 2025, Kennedy replaced all 17 members of the Advisory Committee on Immunization Practices (ACIP), the expert panel that has guided U.S. vaccine recommendations for decades [14]. More than half of the new appointees had never published research on vaccinations [1]. Tom Frieden, who directed the CDC from 2009 to 2017, called the new committee members holders of "bizarre" and "unscientific" views [15].

Kennedy's Case for Reform

Kennedy and his supporters argue these changes are long overdue corrections to an agency that lost the public's confidence during the COVID-19 pandemic. In a Wall Street Journal op-ed, Kennedy wrote that the CDC failed because of "politicized science, bureaucratic inertia and mission creep" [16]. He pointed to specific metrics: only one-third of healthcare workers participated in the 2023-24 fall COVID booster program, and fewer than 10 percent of children under 12 received boosters in 2024-25. "The American people no longer believe the CDC has their best interests at heart," he wrote [16].

Kennedy criticized the agency's budget allocation, noting that only half of its total budget supported its infectious disease mission, and that fewer than one in ten employees were epidemiologists—a staffing ratio he blamed for the agency's pandemic response failures [16]. He framed his actions as eliminating "conflicts of interest and bureaucratic complacency" and applying "gold-standard science to every recommendation" [16].

These arguments draw on real, documented institutional problems. A 2022 Senate investigation found "significant failures" in federal pandemic preparedness and the CDC's initial COVID-19 response, including the botched rollout of diagnostic testing [17]. The CDC's own former director, Rochelle Walensky, acknowledged the agency was "responsible for some pretty dramatic, pretty public mistakes, from testing to data to communications" [18]. Conservative policy organizations like the Heritage Foundation and Paragon Institute had called for narrowing the CDC's expanded mission and increasing congressional oversight well before Kennedy took office [19].

Congress itself acted on bipartisan reform instincts in 2024, requiring for the first time that CDC directors be Senate-confirmed and submit strategic plans to Congress—a measure aimed at increasing accountability [18].

The Measles Test Case

The real-world consequences of the CDC's transformation are playing out in measles wards. U.S. measles cases hit 2,285 in 2025—a 34-year high—with 49 outbreaks reported across 45 jurisdictions [20]. The surge has continued into 2026, with 1,487 confirmed cases reported through March 19 [20]. In November 2025, the Pan American Health Organization declared that the Americas had lost measles elimination status for the first time, meaning the disease is now circulating continuously rather than appearing only in isolated imported cases [21].

Source: CDC Measles Data

Data as of Mar 19, 2026CSV

Ninety-three percent of measles cases have occurred in people who were unvaccinated or did not know their vaccination status [20]. Childhood MMR vaccination coverage has declined from 95.2 percent during the 2019-2020 school year to 92.5 percent during 2024-2025—below the 95 percent threshold needed for herd immunity [21].

Kennedy's reconstituted ACIP and his public skepticism toward vaccine mandates have alarmed epidemiologists who see a direct link between federal messaging and local vaccination decisions. However, the decline in vaccination rates predates Kennedy's tenure as HHS Secretary, beginning during the pandemic years.

Surveillance in the Dark

Beyond measles, the agency's capacity for disease surveillance—the foundational function of identifying and tracking outbreaks—has deteriorated. By October 2025, 38 CDC databases that should have been updated monthly were not current, and by December 2025, only one of those 38 had been updated [22]. These databases cover vaccination surveillance, disease tracking, and epidemiological data that state and local health departments depend on.

The Epidemic Intelligence Service and the Laboratory Leadership Service—programs that train the epidemiologists Kennedy himself noted were too few—were gutted [1]. CDC laboratories for sexually transmitted diseases and hepatitis were eliminated, despite the CDC being the only federal entity with the capacity to test for rarer forms of these diseases [23].

One current employee told reporters: "It's like a web and when you rip out part of that, you can't expect it to work the same as before" [1]. Stations are "choosing not to do certain things because there aren't enough resources," the employee said [1].

Nine Former Directors Sound the Alarm

In September 2025, nine former CDC directors and acting directors—spanning administrations from both parties—published a joint essay in The New York Times calling Kennedy's leadership "unlike anything our country has ever experienced" [24]. The signatories included William Foege, David Satcher, Tom Frieden, Rochelle Walensky, and Mandy Cohen. They warned that Kennedy had "canceled investments in promising medical research that will leave us ill prepared for future health emergencies," "replaced experts on federal health advisory committees with unqualified individuals who share his dangerous and unscientific views," and "announced the end of U.S. support for global vaccination programs that protect millions of children" [24].

Bloomberg Law reported that the CDC's ongoing overhaul "adds risk to crisis response," noting the agency's diminished capacity to mount a coordinated federal response to an emerging infectious disease [25].

The Trust Paradox

Kennedy staked his tenure on the promise of restoring public trust in America's health agencies. By his own metric, that effort is failing. A January 2026 KFF survey found that 47 percent of Americans trust the CDC "a great deal" or "a fair amount" to provide reliable vaccine information—down approximately 10 percentage points since the start of Trump's second term [26]. Even among supporters of Kennedy's Make America Healthy Again movement, fewer than half said they trust the CDC or FDA to make recommendations about childhood vaccine schedules [26].

More than 1,000 current and former HHS employees signed a letter in September 2025 calling on Kennedy to resign, accusing him of "compromising the health of this nation" [27]. The letter represented a rare act of collective dissent within the federal workforce.

What Comes Next

The question facing Congress, the courts, and the public is whether the CDC's remaining capacity is sufficient to meet the next public health emergency. The proposed budget awaits congressional action. Federal judges have blocked some of the most aggressive funding clawbacks [11]. The measles outbreaks continue to grow.

Kennedy's defenders point to genuine pre-existing institutional failures and argue that entrenched bureaucracies resist any change, necessary or otherwise. His critics—including nearly every living former leader of the agency—counter that what is underway is not reform but dismantlement, and that the consequences will be measured in preventable illness and death.

The CDC, an agency founded in 1946 to fight malaria, now faces an existential question about its role and capacity. The answer will be determined not by rhetoric from either side but by what happens when the next outbreak, the next pandemic, or the next public health crisis arrives—and whether anyone is left to respond.