The First Circuit vaccine policy dispute returned to the spotlight Tuesday as the administration asked a Boston-based appeals panel to lift a federal court order that paused sweeping changes to childhood immunization guidance.
In March, U.S. District Judge Brian Murphy granted a preliminary injunction in favor of medical organizations that sued Health and Human Services Secretary Robert F. Kennedy Jr. over his moves to rework federal vaccine policy. The order temporarily blocked changes to the childhood immunization schedule and stayed all decisions made by Kennedy’s appointees to the Centers for Disease Control and Prevention’s Advisory Committee on Immunization Practices between June 2025 and January 2026. The appointments themselves were also put on hold.
In a 45-page ruling, Murphy, a Joe Biden appointee, found the government had set aside established procedures and undermined the integrity of agencies charged with providing expert guidance on vaccine use and broader public health matters.
First Circuit vaccine policy arguments
According to court filings, the contested measures under Kennedy’s leadership included removing broad recommendations from the childhood vaccine schedule, restricting access to Covid-19 shots, and overhauling the ACIP, the committee that traditionally shapes vaccine policy.
The American Academy of Pediatrics and other public health groups filed suit in July 2025, arguing that the rollback endangers children and pregnant women, whom they described as especially vulnerable to severe infections from Covid-19 and other viruses. Limiting access to vaccines, they said, is ethically indefensible.
On appeal, government lawyers argued that the plaintiffs lack standing because their challenges do not target a reviewable final agency action by the CDC. Department of Justice attorney Matthew Charles Zorn told the panel there was no discrete agency action to support the injunction, urging the court to vacate the stay and send the case back for further explanation.
Public health groups asked the First Circuit to affirm the injunction. Attorney Andrew Pincus said the government seeks a ruling that could later be used to attack CDC recommendations, adding that the district court carefully evaluated the relevant issues. Responding to questions from U.S. Circuit Judge David Barron, Pincus characterized the ruling as a preliminary stay that paused the appointments but allowed the agency to try again without the court itself deciding which appointees should be removed.
Pressed by U.S. Circuit Judge Joshua Dunlap to identify a final agency action reviewable under the Administrative Procedure Act, Pincus cited a June 2025 op-ed by Kennedy outlining plans to dramatically change ACIP. He also pointed to the institution of the reconstituted committee as a separate final action. The plaintiffs allege Kennedy made false accusations against 17 sitting ACIP members, claiming they had persistent conflicts of interest, acted as a rubber stamp for any vaccine, and were aligned with industry interests.
U.S. Circuit Judge William Kayatta completed the three-judge panel. The court did not indicate when it would issue a decision.
Changes to CDC recommendations at issue
The dispute follows CDC actions late last year and earlier this year. In December, the agency dropped its recommendation for a universal hepatitis B birth dose, a vaccine that is up to 90% effective at preventing perinatal infection when given within 24 hours of birth. The CDC subsequently shifted several vaccines from the recommended childhood schedule to use for high-risk patients or in shared clinical decisionmaking, including those for rotavirus, meningococcal disease, hepatitis A, hepatitis B, influenza, Covid-19, and RSV.