Health and Human Services Secretary Robert F. Kennedy Jr. has had a busy few months. He fired the director of the Centers for Disease Control and Prevention, purged the agency's vaccine advisory committee, and included among the group's new members appointees who espouse anti-vaccine views.
The leadership upheavals, which he says will restore trust in federal health agencies, have shaken the confidence many states have in the CDC and led to the fracturing of a national, cohesive immunization policy that's endured for three decades.
States and medical societies that long worked in concert with the CDC are breaking with federal recommendations, saying they no longer have faith in them amid the turmoil and Kennedy's criticism of vaccines. Roughly seven months after Kennedy's nomination was confirmed, they're rushing to draft or release their own vaccine recommendations, while new groups are forming to issue immunization guidance and advice.
How the new system will work is still being hammered out. Vaccine recommendations from states, medical societies, and other groups are likely to diverge, creating dueling guidance and requirements. Schoolchildren in New York may still generally need immunizations, for example, while others in places such as Florida may not need many vaccines.
There are potential financial ramifications too, because historically, private insurers, Medicaid, and Medicare have generally covered only vaccines recommended by the federal government. If the CDC and its advisory group, which began a two-day meeting Sept. 18 in Atlanta, stop recommending certain vaccines, hundreds of millions of people could wind up paying for shots that previously cost them nothing. Some states are already taking steps to prevent that from happening, which means where people live could determine if they will face costs.
"You're seeing a proliferation of recommendations, and the recommendations by everybody are different from the CDC," said Michael Osterholm, a University of Minnesota epidemiologist who launched an ad hoc group that provides vaccine guidance. "States and medical societies are basing their recommendations on science. The recommendations out of CDC are magic, smoke, and mirrors."
Kennedy has defended changes at the CDC and the revamping of the vaccine committee as necessary, saying previous advisory panel members had conflicts of interest and agency leadership botched its pandemic response.
The CDC is "the most corrupt agency at HHS, and maybe the government," Kennedy said at a Sept. 4 Senate committee hearing. Susan Monarez, the ousted CDC director, testified Sept. 17 at another Senate hearing about how Kennedy told her to preapprove vaccine recommendations from the advisory panel or be fired.
Kennedy has said HHS also plans to investigate vaccine injuries he says are not thoroughly tracked or investigated. The CDC investigates injuries that are reported by providers or patients, but Kennedy has said he wants to recast the entire program. The Food and Drug Administration is already looking into cases of children who died following covid-19 vaccination.
HHS didn't return an email seeking comment.
The actions by states, medical societies, and other groups reflect a mounting lack of confidence in federal leadership, public health leaders say, and the break from the CDC is happening at a rapid clip.
The Democratic governors of California, Hawaii, Oregon, and Washington — fashioning themselves as the West Coast Health Alliance — are coordinating to develop vaccine recommendations that won't necessarily follow those from the CDC. The governors said in a joint statement that the CDC shake-up has "impaired the agency's capacity to prepare the nation for respiratory virus season and other public health challenges" and this week issued 2025-26 guidance for vaccination against viruses such as covid, influenza, and respiratory syncytial virus.
A group of northeastern states are exploring a similar collaborative.
"The worst thing that could happen is that we have 50 different recommendations for the covid vaccine. That will destroy public health," said Massachusetts Public Health Commissioner Robbie Goldstein, who has been involved with the effort. He's also spoken with leaders of the West Coast alliance. “I’m really hopeful that we do come together in larger and larger collaboratives with the same recommendations or very similar recommendations,” he said while speaking to a group of reporters this month.
And medical societies such as the American Academy of Pediatrics are releasing covid vaccine recommendations that diverge for the first time from the CDC's guidance.
Some states are seizing on the split to ensure access to shots. Massachusetts is requiring insurers to cover vaccines recommended by the state health department rather than paying only for those suggested by the CDC, making it the first state to guarantee such continued coverage. AHIP, a trade group representing insurers, said on Sept. 16 that health plans will cover immunizations, including updated formulations of covid and flu vaccines, that were recommended by the CDC panel as of Sept. 1 with no cost sharing through the end of 2026.
Pennsylvania is allowing pharmacists to give covid vaccines even if they're not recommended by the federal agency. Instead, they can follow recommendations from the pediatric academy and other medical groups.
Florida, meanwhile, plans to drop requirements for schoolchildren to get immunizations against chickenpox, meningitis, hepatitis B, and some other diseases. State lawmakers would need to take action to end mandates for all vaccines.
Joseph Ladapo, the state's surgeon general, said in a Sept. 3 press conference that any vaccine requirement is wrong and "drips with disdain and slavery."
Some doctors criticize the decision as a dangerous step backward.
"This is a terrifying decision that puts our children's lives at risk," said Richard Besser, former acting director of the CDC, in an emailed statement.
The first school vaccine mandate was rolled out in the 1850s in Massachusetts, for smallpox. While all states have vaccine requirements for schoolchildren, immunization rates for kindergarten students declined while cases of vaccine-preventable measles and whooping cough surged in 2024 and 2025.
Rochelle Walensky, the Biden administration's first CDC director, warned of the "polarization" of state-by-state approaches. "It's like your head is in the oven and your feet are in the freezer and, on average, we're at 95% vaccination. That doesn't work in measles — every place has to be at 95% vaccination." She was referring to the proportion of a population that needs to be vaccinated to provide herd immunity.
Kennedy's actions have thrust vaccines center stage and made him fodder for comedy. The Marsh Family, a British musical group, released a parody on Sept. 7 of Paul Simon's "Me and Julio Down by the Schoolyard," with the chorus, "We'll see measles and polio down in the schoolyard."
HBO comedian Bill Maher said the CDC could be known by the title "Disease" during a recent episode of his show. And Stephen Colbert used his monologue on "The Late Show with Stephen Colbert" to weigh in on the revamped vaccine advisory group, calling its new members the "crème de la cuckoo."
President Donald Trump has defended Kennedy, telling reporters "he means very well," even as Trump said on Sept. 5 that "you have some vaccines that are so amazing." Trump has repeatedly expressed pride in Operation Warp Speed, a government initiative during Trump's previous administration that rapidly developed covid vaccines. But he's also promoted a discredited theory linking vaccines and autism.
The White House did not respond to a request for comment.
The Trump administration already narrowed recommendations for the covid vaccine despite no new safety risks with the shots, although medical societies are continuing to recommend them for most people. The gulf is expected to widen as the agency's advisory group reviews whether to change its guidance on a number of pediatric vaccines.
Other groups are also trying to provide vaccine and public health guidance, driven in part by concerns that Kennedy and other federal health leaders will make policy decisions and statements not grounded in science. Kennedy has promoted claims that aluminum, used in many vaccines, is linked to allergies, despite a lack of evidence for the claims. A Danish study, in fact, found aluminum was not linked to chronic disease, but Kennedy said the study's supplemental data indicated it caused harm. The journal that published the study defended the findings.
Current and former CDC and HHS staffers, along with public health academics and retired health officials, have formed the National Public Health Coalition, a nonprofit to endorse recommendations and provide guidance on policy issues. They plan to partner with state and local health departments.
"A real benefit of the National Public Health Coalition is we are made up of current and former CDC and HHS folks, people who have deep knowledge of what government programs for public health look like, and what improvements are needed," said Abigail Tighe, the group's executive director.
Another new group is Grandparents for Vaccines, which bills itself as a volunteer-led effort to raise awareness about vaccines. And the Vaccine Integrity Project was launched in April by the University of Minnesota's infectious disease center, to review evidence for medical societies on the safety and effectiveness of vaccines.
"We're going to continue to help wherever we can to address misinformation,” said Osterholm, the center's leader.
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