CDC vaccine policy recommendations grind to a halt under Health
Secretary Kennedy
[September 26, 2026]
By MIKE STOBBE
NEW YORK (AP) — The Food and Drug Administration recently approved a new
flu vaccine that tested well in older adults. But the federal agency
responsible for telling doctors and the general public how to use it has
made no recommendation on it.
The Centers for Disease Control and Prevention’s inaction on the
mFlusiva vaccine marks a break in longstanding practice. It’s also an
example of how the agency’s vaccine review-and-recommendation process
has been blown up in the past year, grinding decision-making to a halt.
Efforts by vaccine-wary officials in President Donald Trump's
administration to scale back shot recommendations have been put on hold.
Federal guidance on new vaccines has stopped. And public discussion of
vaccine policy questions that might cross political divides — including
whether there’s solid evidence to justify giving fewer shots to kids —
has diminished.
Health Secretary Robert F. Kennedy Jr.’s crusade to upend vaccine policy
and the legal action opposing it have disrupted longstanding systems
that deliver crucial health guidance to Americans, affecting whether
people are getting the best available protection against
vaccine-preventable diseases.
“We find ourselves at a point where even if credible evidence (for a new
vaccine policy) has reached a tipping point, we don’t have an obvious
mechanism that can formalize that change,” said Jason Schwartz, a Yale
University health policy researcher who studies government health
agencies.
Many in the medical field praised a court ruling that halted
Kennedy’s changes
For 60 years, the Advisory Committee on Immunization Practices guided
the CDC’s vaccine recommendations. The committee met publicly, reviewed
vaccine data and sought input from various health groups. The panel
voted on recommendations that went to the CDC director, who almost
always adopted them as the government’s guidance, leading public and
private insurers to pay for the shots.
Trump, a Republican, appointed Kennedy to oversee federal health
agencies, including the CDC. Kennedy last year dismissed the committee
and replaced it with a group that included several anti-vaccine voices.
Controversial decisions followed, leading to a lawsuit from the American
Academy of Pediatrics and some other medical groups.
In March, a federal judge said Kennedy likely violated federal
procedures, stopped Kennedy’s panel from holding further meetings and
suspended Kennedy’s decision to reduce the number of vaccines
recommended for children.
Many in the medical and public health communities celebrated the
decision and took the order as a respite from what they saw as the Trump
administration’s assault on vaccines.
Dr. Jason Goldman, president of the American College of Physicians, said
he hoped “it will mean a return to a transparent and evidence-driven
process that safeguards the health of all communities and the best
interests of our patients.”
In reality, the process stalled and splintered
With Kennedy’s committee shut down by the court order, doctors’ groups
that used to collaborate with the ACIP have gone their own way. Working
with a University of Minnesota researcher, they have debated — not
publicly — the kind of medical evidence formerly presented at ACIP
meetings and issued their own recommendations.
The trade association for private health insurers decided to heed the
medical societies’ choices, and the insurers have continued to pay for
shots recommended by those organizations.
Many of the groups’ recommendations match prior ones made by ACIP and
the CDC before Kennedy’s arrival. But they also made their own updates.
For example, ACIP previously recommended that a new shot be given to
women late in pregnancy: a vaccine against respiratory syncytial virus,
or RSV, which can be dangerous to newborns. The government panel
recommended that the vaccine be given between September and January in
most of the U.S., to coincide with the time of year when RSV infections
are most common.
But RSV season sometimes remains active longer. For that reason, the
medical groups recently said the shot should be offered to those women
through the beginning of March.
“We all recognized this needs to evolve,” Chris Regal, director of
clinical innovation at America’s Health Insurance Plans, the health
insurance trade association, said in a recent webinar.
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Health and Human Services Secretary Robert F. Kennedy Jr. listens as
President Donald Trump speaks during an event about healthcare in
the Oval Office of the White House, Friday Sept. 18, 2026, in
Washington. (AP Photo/Jacquelyn Martin)
 The official CDC guidance remains
unchanged.
Unanswered vaccine issues are piling up
The mFlusiva flu shot is another example of the unusual way vaccine
policy updates have stalled.
The shot is the first flu vaccine made with the mRNA technology that
was key to ending the COVID-19 pandemic. Kennedy has criticized mRNA
vaccines and last year canceled contracts for the development of new
ones. The shots also took a tortuous path through the FDA, which
finally granted full approval in people ages 50 to 64.
But the CDC this month quietly posted that it has decided to
maintain its flu vaccine endorsements from last year due to “legal
uncertainties and inquiries.” That means mFlusiva is not among the
listed flu vaccines recommended to the public this fall.
The medical societies are recommending it as an option, however.
Another ACIP function was to vote on whether certain vaccines should
be covered by Vaccines for Children, a government program that pays
for shots for children who have no health insurance.
The FDA approved updated COVID-19 vaccines, but as the summer
dragged on — and fall vaccination campaigns got underway — the
government would not say if the VFC program will pay for those
shots. It was only this week that officials confirmed orders could
be placed through that program.
HPV vaccine reassessment is derailed
Another question concerns the HPV vaccine, given to preteens to
prevent certain cancers.
Two HPV shots are recommended, but some recent research has
suggested that perhaps one shot could be enough — at least for
girls. Indeed, in 2024 the ACIP formed a working group to begin a
reassessment of the recommendations.
That work was derailed when Kennedy fired the entire committee. In
January, he decided on his own to order that the number of
recommended doses be reduced to one as part of a dramatic
contraction of the childhood vaccination schedule. His decision was
suspended by the judge’s order.
Experts are trying to better understand the timing and the duration
of protection from just one dose, particularly in boys. The American
Academy of Pediatrics is weighing a change to its HPV vaccination
recommendations and could reach a conclusion later this year, said
the AAP’s Dr. James Campbell.
It’s possible that the medical societies will end up agreeing with
Kennedy on just how many HPV shots make sense. But that might not
necessarily clear up the current mess, Schwartz said.
“The credibility of the Trump administration, when it comes to
vaccine recommendations, is so compromised in the eyes of the
mainstream medical and public health communities,” he said, “that
even recommendations that might align with where the public health
community was trending are likely to be viewed with skepticism or
distrust.”
Meanwhile, the Trump administration is considering changing the
federal government's categories for vaccine recommendations,
although a specific proposal has not been released and a Department
of Health and Human Services spokesperson did not respond to
questions about what is being contemplated. Public comments were due
earlier this week.
An alliance of 15 Democratic state governors said the proposed
changes are likely to increase confusion and administrative
complexity.
“It’s Governors and their residents who bear the brunt of any
increased disease outbreaks due to confusion related to hastily made
federal changes,” Angela Botticella, managing director of the
Governors Public Health Alliance, said in a statement.
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