A federal judge has given the green light for a lawsuit challenging Health and Human Services Secretary Robert F. Kennedy Jr.’s COVID-19 vaccine recommendations to proceed.

In a 22-page ruling, U.S. District Judge Brian Murphy affirmed that the plaintiffs, including the American Academy of Pediatrics (AAP) and various medical associations, have a legitimate basis for their case, dismissing Kennedy’s attempt to have it dismissed.

The legal dispute originates from May 2025, following Kennedy’s directive to the Centers for Disease Control and Prevention (CDC) to eliminate the routine recommendation for COVID-19 vaccination for pregnant women and healthy children. This led the CDC to adjust its guidance to a “Shared Clinical Decision Making” (SCDM) status, which, according to the AAP, is generally used for vaccines where the risk versus benefit is not straightforward.

Changes continued within the Department of Health and Human Services (HHS). On June 9, 2025, Kennedy dismissed all 17 members of the Advisory Committee on Immunization Practices (ACIP), which is responsible for creating evidence-based vaccine recommendations. He replaced them with new members, whom the AAP argues lack qualifications and were selected due to their alignment with Kennedy’s perceived “anti-vaccine agenda.”

Furthermore, Kennedy removed participation from the AAP and similar groups in ACIP workgroups, citing them as “special interest groups,” as noted by Judge Murphy. In a subsequent move three months later, the restructured ACIP altered the COVID vaccine recommendation for adults under 65 to an SCDM designation.

On July 7, 2025, the AAP, alongside other medical associations and individuals impacted by these changes, filed a lawsuit. They claim the adjustments to vaccine recommendations and ACIP’s restructuring breach the Administrative Procedure Act (APA) and Federal Advisory Committee Act (FACA) rules. They argue Kennedy’s actions forced them to allocate resources to create new frameworks and guidance to serve their members effectively.

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.