Federal judge blocks HHS vaccine changes, citing a lack of scientific rigor

A US District Court sided with major medical institutions that the changes pushed by US Health Secretary Robert F. Kennedy Jr. were unlawful partly because they valued politics over expertise.

A federal judge on Monday blocked major changes to the federal childhood vaccine schedule that US Health Secretary Robert Kennedy Jr. helped push through over the objections of nearly every medical association in the country. 

Judge Brian Murphy, of the US District Court for the District of Massachusetts, ruled that the changes violated a rigorous scientific and procedural precedent, siding with the medical associations who sued over the changes, including the American Academy of Pediatrics (AAP), that they were unlawful. 

Murphy, a Biden appointee, also ruled that Kennedy had improperly removed previous experts from the Advisory Committee on Immunization Practices (ACIP), a federal panel that helps steer vaccine policy, and replaced them with political appointees. Murphy temporarily halted all decisions the panel has made since the staffing changes.

The new recommendations pushed by Kennedy did not ban any vaccines, but they removed six widely-used and effective vaccines from the list of recommended routine childhood inoculations, including the seasonal flu shot. Medical associations, as well as several doctors who spoke to Cardinal & Pine, warned that the Kennedy changes would lower overall vaccination rates and lead to the resurgence of some serious diseases that had been nearly eradicated. They could have also made flu seasons far deadlier for children.

Murphy wrote in this ruling that vaccine policy had historically been set by “an apparatus that marries the rigors of science with the execution and force of the United States government.”

But by basing the recent changes on politics rather than science, Murphy wrote, the Trump administration violated that marriage. 

“The Government bypassed ACIP to change the immunization schedules, which is both a technical, procedural failure itself and a strong indication of something more fundamentally problematic: an abandonment of the technical knowledge and expertise embodied by that committee,” Murphy wrote.

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“Second, the Government removed all duly appointed members of ACIP and summarily replaced them without undertaking any of the rigorous screening that had been the hallmark of ACIP member selection for decades.”

He added: “This procedural failure highlights the very reasons why procedures exist and raises a substantial likelihood that the newly appointed ACIP fails to comport with governing law.”

The Trump administration is likely to appeal the ruling, but the AAP applauded the ruling as “a historic and welcome outcome for children, communities, and pediatricians everywhere.”

“This decision effectively means that a science-based process for developing immunization recommendations is not to be trifled with and represents a critical step to restoring scientific decision-making to federal vaccine policy that has kept children healthy for years,” Dr. Andrew Racine, President, American Academy of Pediatrics, said in a press release.

What were the changes?

The vaccines for measles, polio, and chickenpox were still universally recommended under the Kennedy panel, but the vaccines for RSV, Hepatitis A and B, and meningococcal disease were switched from universal to only suggested for “high-risk groups.” 

And flu, COVID-19 virus, and rotavirus vaccines were considered entirely optional. 

None of these diseases are pleasant and each can be especially hard on children. Many of them can lead to permanent damage. And all of them are preventable with vaccines. 

Dr. Michael Smith, division chief of pediatric infectious diseases at the Duke University School of Medicine, told Cardinal & Pine soon after that rotavirus can be especially grisly for children, but that the vaccine, which became widely used starting in 2006, all but eradicated the disease.

RELATED: Looking for reliable resources about childhood vaccines? Start here. 

Before the current rotavirus vaccines were added to the schedule in 2006 and 2008, Smith said, 10 or 20  kids would come to the ER each night during rotavirus season with severe dehydration, intense vomiting, and “horrible diarrhea.” 

After the vaccines, he said, “that disease went away.” At Duke University, most of the resident physicians and medical students “have never seen a single case,” he said.

Dr. Smith said he was especially worried that the flu shot was no longer broadly recommended.

Like in most of the nation, the current and previous flu seasons have been brutal in North Carolina. Cases are up, and there have been hundreds of deaths across the country, building upon the 2024-2025 flu season in which more children died from flu complications than in any other season over the prior 16 years.

There have been nine pediatric flu deaths in North Carolina this flu season. 

“Approximately half of the children who died from influenza last season did not have an underlying medical condition, and 89% were not fully vaccinated,” the North Carolina Department of Health and Human Services says.