Left: U.S. District Judge Brian Murphy of the District of Massachusetts in April, 2024 (Instagram/Senate Judiciary Democrats). Right: Robert F. Kennedy Jr. hosts a fireside chat (John Lamparski/Sipa USA/Sipa via AP Images).
A lawsuit challenging Health and Human Services Secretary Robert F. Kennedy Jr.'s recommendations on the COVID-19 vaccine can move forward, a federal judge has ruled.
U.S. District Judge Brian Murphy wrote in his 22-page order that the individual people and professional medical associations — led by the American Academy of Pediatrics (AAP) — that filed suit were well within their right to do so, denying a challenge from Kennedy to have the complaint thrown out.
The case can be traced back to May 2025, when Kennedy announced an order for the Centers for Disease Control and Prevention (CDC) "to remove from the routine CDC Schedules the recommendation that pregnant women and 'healthy' children receive the COVID vaccine." The agency subsequently changed the routine recommendation to a "Shared Clinical Decision Making" (SCDM) designation, which the AAP says is "typically reserved for vaccines where the risk/benefit analysis is less clear or complex."
The Department of Health and Human Services (HHS) continued making changes. On June 9, 2025, Kennedy fired all 17 existing members of the Advisory Committee on Immunization Practices (ACIP), a federal advisory committee established under the Federal Advisory Committee Act (FACA) to create "evidence-based recommendations for the use of vaccines." He then appointed new members, whom the AAP alleges are unqualified and were only chosen "based on the candidates' alignment with Secretary Kennedy's 'anti-vaccine agenda.'"
The HHS secretary also discontinued the participation of AAP and other similar organizations from ACIP workgroups "on the stated basis" that they constitute "special interest groups," as Murphy recalls. Three months later, the newly-constructed ACIP went further, voting to change the COVID vaccine recommendation for adults under the age of 65 from a routine recommendation to an SCDM designation.
On July 7, 2025, the AAP and other medical associations and individuals allegedly affected by the directives filed their lawsuit, arguing the changes to the vaccine recommendations and ACIP violated the Administrative Procedure Act (APA), the statute governing how federal agencies operate, as well as FACA guidelines. They contended that Kennedy's changes forced them to "divert resources to develop new infrastructures, processes, and guidance to fulfill their mission to their members."
The plaintiffs were scathing in their complaint, saying Kennedy's directives "caused confusion and uncertainty" as to whether people "can — or even should — get the Covid vaccine" and produced "increasing distrust of doctors' advice to their patients to get vaccinated, thus damaging the patient-physician relationship and inhibiting the ability of health care providers to practice according to the standard of care required of them."
"The solution to the damage that the Directive has caused across the entire vaccine ecosystem is to vacate the Directive and order the Secretary to restore the recommendations" from before, they wrote in an amended complaint filed on July 23. As Murphy recounts, "[a]mong various theories of harm, AAP has alleged that it has had to devote significant time and resources to counseling many of AAP's 67,000 members in light of the Challenged Actions. This work has allegedly come at the cost of AAP's diverting resources away from its usual tasks and initiatives aimed at children's health."
Kennedy and HHS subsequently, on Sept. 3, 2025, filed a motion to have the lawsuit dismissed. They contended that AAP's stated "educational and advocacy work" is simply "a continuation of [its] 'ongoing activities.'"
The judge, a Joe Biden appointee, found this argument unconvincing.
"Defendants mischaracterize AAP's immunization schedules by calling them mere 'educational and advocacy work,'" he wrote. "AAP's recommendations to physicians on vaccine use predate the creation of ACIP by more than 25 years. There is no basis for the Court at this juncture to discredit that characterization or discount the importance such work has on the organization's efforts to support its members in furtherance of its mission."
"In sum, this type of diversion of resources goes beyond mere advocacy as to be sufficient for organizational standing," the Boston-based judge added.
Murphy also touched upon the AAP's claim that the new ACIP members — of whom all but one has reportedly "professed strong opposition to the COVID vaccine and/or mRNA vaccines generally" — were appointed by Kennedy because of their views on vaccines and the secretary's alleged biases.
"[E]ven if the members were not appointed solely based on their views, it does not follow that the membership is fairly balanced," the judge wrote. "Plaintiffs allege that these appointments skewed the composition of ACIP in favor of COVID-vaccine and/or mRNA-vaccine deniers in order to comport with Secretary Kennedy's personal views. Given ACIP's role in providing recommendations on vaccines to the CDC, the Court cannot conclude that views supportive of the COVID vaccine and/or mRNA vaccines more generally are not the type of legitimate views that FACA requires balancing in appointing members."
"At this stage of the litigation, Plaintiffs have plausibly alleged that the current ACIP composition does not comport with FACA's requirements," he continued. "Thus, the allegations are sufficient to survive a motion to dismiss."
Murphy ordered on Tuesday that the plaintiffs and defendants update him with a case management plan, including a proposed briefing schedule for any contemplated motions.
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