Health and Human Services secretary Robert F. Kennedy Jr. has pursued an aggressive overhaul of federal vaccine guidance and infrastructure since he took office a little over a year ago. Now, his agenda is on hold after a federal judge blocked many of those changes and as reports surface that the White House is reining in his anti-vaccine rhetoric ahead of the midterm elections.

What’s next for US vaccine policy will depend on the outcome of a federal court case, and whether Kennedy is allowed to resume his crusade against vaccines after November. Even if the Trump administration pivots to a more science-backed approach to vaccines, public health experts worry about the long-term effects of Kennedy’s tenure to date.

“It’s unknown what these ramifications are going to look like,” says Syra Madad, chief biopreparedness officer at NYC Health + Hospitals, the largest municipal health care system in the US. “Already, we’re seeing more vaccine hesitancy. We’re seeing the rise of vaccine-preventable illnesses such as measles.”

A longtime vaccine conspiracy theorist, Kennedy dropped Covid-19 vaccine recommendations for healthy children and pregnant women last May. Shortly after, he ousted all 17 previous members of the Advisory Committee on Immunization Practices, or ACIP, which makes vaccine recommendations to the Centers for Disease Control and Prevention. After he appointed new members with a history of criticizing vaccines, the reconstituted panel voted in December to end the recommendation for a universal birth dose of the hepatitis B vaccine, guidance that had been in place since 1991.

In January, Kennedy announced sweeping changes to the childhood immunization schedule, bypassing his own vaccine advisory panel and reducing the number of routine vaccines from 17 to 11 without providing any scientific rationale for doing so.

A lawsuit filed by the American Academy of Pediatrics and other medical groups challenged these changes. A federal judge ruled in March that the new ACIP members were unlawfully appointed, voiding their previous actions. The decision also paused implementation of Kennedy’s changes to the childhood vaccination schedule, since he did not consult ACIP first.

The Trump administration has said it will appeal, throwing vaccine policy into limbo. “HHS looks forward to this judge’s decision being overturned just like his other attempts to keep the Trump administration from governing,” spokesman Andrew Nixon told WIRED in an email.

In recent weeks, Kennedy has toned down his messaging around vaccines, focusing instead on nutrition and microplastics and announcing a new podcast. Robert Malone, one of Kennedy’s hand-picked members for ACIP, who stepped down in March, said on a conservative podcast that Kennedy was ordered by a White House adviser to “shut down” any discussions about vaccines ahead of the mid-term elections in November, suggesting that Kennedy’s anti-vaccine views are unpopular with voters.

How the US makes decisions about vaccines for the rest of President Trump’s term is an open question. ACIP recommendations become federal policy when they are adopted by the CDC director, but Kennedy fired previous CDC director Susan Monarez, allegedly because she would not rubber-stamp his vaccine changes. The position has been open since August, with National Institutes of Health director Jay Bhattacharya currently running the agency. Despite his boss’s anti-vaccine views, Bhattacharya recently told CDC staffers that it is “absolutely vital” to get the measles vaccine.

“Vaccination recommendations are frozen in amber to the time before Kennedy took office,” says Elizabeth Jacobs, an epidemiologist at the University of Arizona and a founding member of Defend Public Health, a grassroots organization that formed in late 2024 after Kennedy’s nomination.