A Federal Court Blocks RFK Jr.’s Anti-Vaccine Agenda – But the Threat to Children Is Not Over

There is some genuinely good news to share: a rare commodity in the current policy environment.

On March 16, 2026, U.S. District Judge Brian Murphy issued a sweeping ruling in American Academy of Pediatrics v. Kennedy that temporarily blocked several major vaccine policy changes Department of Health and Human Services (HHS) Secretary Robert F. Kennedy, Jr. has made since taking office. The ruling is a strong indictment and reversal, even if temporary, as to how the Trump Administration has treated children’s health as a political instrument.

But the good news does not end there.

Even before the court acted, 30 states had already moved to establish their own vaccination schedules, refusing to follow Secretary Kennedy’s dismantling of federal guidance of the immunization schedule. That kind of state-level resistance, which I’ll return to, is a preview of something larger we need to build: a governing framework that prioritizes the needs of children whose well-being cannot be held hostage to federal negligence and abandonment.

And then there is the bad news, because there always seems to be bad news right now.

Unfortunately, vaccination rates are dropping. Children are dying from preventable diseases. And the so-called “Make America Healthy Again” (MAHA) movement, which has the ear of this Administration, is not satisfied with what Kennedy has already done – it wants to eliminate the childhood vaccination schedule entirely.

Let’s review where vaccine policy currently stands.

Judge Murphy opened his 45-page opinion with a Carl Sagan quote that set the tone for everything that followed:

“Science,” like law, “is far from a perfect instrument of knowledge.” History is littered with once-universal truths that have since come under scrutiny. Nevertheless, science is still “the best we have. In this respect, as in many others, it’s like democracy.”

Judge Murphy’s ruling is about both the substance of what this Administration is doing to children’s health and the procedural contempt with which it has done so.

The central finding is this: HHS reconstituted the Advisory Committee on Immunization Practices (ACIP) in a manner that violated the procedures that were put into place, as required by law.

Furthermore, HHS has bypassed ACIP to change 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,” wrote Judge Murphy.

Since its creation in 1964, ACIP has provided the scientific backbone of U.S. vaccine policy. In light of its expertise required at ACIP, Congress, in multiple statutes, has tied insurance coverage obligations, Medicaid benefits, veterans’ benefits, and the Vaccines for Children (VFC) program to ACIP’s recommendations.

When Secretary Kennedy fired all 17 members of ACIP in June 2025 and replaced them through a rushed, informal process – and then used his reconstituted committee to gut the childhood vaccine schedule – he violated the procedures required by federal law to promote science over politics.

The January 2026 memo at the heart of the case, signed by then-acting CDC Director Jim O’Neill, introduced a new immunization schedule that reduced the number of childhood vaccinations recommended as ‘routine’ from seventeen to eleven – all without any ACIP involvement, public comment, or the evidence-based review process that has governed these decisions for decades.

The judge was unambiguous: Director O’Neill issued the January 2026 Memo without sufficiently consulting ACIP. Therefore, he lacked authority to issue the January 2026 Memo and, in so doing, acted in violation of the Administrative Procedure Act (APA).

On the reconstituted ACIP itself, the ruling is even more pointed. The court found that of the fifteen members currently on ACIP, even under the most generous reading, only six appear to have any meaningful experience in vaccines — the very focus of ACIP.

The court also exposed the limits of the administration’s legal theory in an exchange that deserves to be read in its entirety. The judge asked whether, under the government’s argument that vaccine policy is entirely committed to agency discretion and unreviewable by courts, the CDC could recommend that people skip vaccines and go have lunch with someone who has measles instead. The government’s lawyer said yes – that too would be unreviewable. The Court disagreed.

Judge Murphy noted that Congress specifically passed laws that direct the Secretary to fund:

“…a national, evidence-based campaign to increase awareness and knowledge of the safety and effectiveness of vaccines for the prevention and control of diseases, combat misinformation about vaccines, and disseminate scientific and evidence-based vaccine-related information, with the goal of increasing rates of vaccination across all ages, as applicable, particularly in communities with low rates of vaccination, to reduce and eliminate vaccine-preventable diseases.”

The Judge added:

It would be quite strange for Congress, in one statute, to authorize the Secretary to “assist” states by encouraging the spread of communicable diseases, while, in another statute, requiring the Secretary to work toward “eliminat[ing]” to spread of communicable diseases.

Consequently, the Judge issued stays to HHS’s January 2026 memo revising the Centers for Disease Control and Prevention’s (CDC) childhood immunization schedule, HHS’s appointments to ACIP, and all votes taken by the reconstituted ACIP.

The federal vaccine recommendations in place before June 2025 are now back in effect – for the moment. The hepatitis B birth dose recommendation is restored. Insurance coverage obligations are reinstated. The scheduled March 18–19 ACIP meeting, which was expected to take votes on further restricting the Vaccines for Children program, did not proceed.

This is a significant win, and it deserves to be celebrated.

As the Center for Infectious Disease Research and Policy (CIDRAP) explains:

Routine childhood vaccines that had been previously downgraded or restricted regain their status as standard recommendations. Insurance coverage at no out-of-pocket cost remains in place because it is tied to ACIP recommendations under federal law, and major insurers had already committed to honoring the pre-change schedule through the end of 2026.

But it is preliminary. The Administration is likely to appeal the decision, and this case may work its way to the First Circuit and possibly beyond. In the meantime, the Administration will also likely reconstitute ACIP with new problematic appointees.

At any rate, we can expect “one battle after another.”

Even before the court acted, the country’s public health infrastructure was not simply accepting federal changes to vaccination schedules that threatened child health.

As of early March, 30 states have announced that they are no longer following CDC recommendations as their benchmark for some or all childhood vaccines and will instead rely on non-federal experts, older versions of the vaccine schedule, or allow their health authorities to determine recommendations based on the latest science and evidence.

Notably, while most of these states have Democratic governors, five have Republican governors – demonstrating that the political instinct to protect children’s health crosses partisan lines when the stakes become concrete.

Colorado became the latest example, passing legislation on the same day as Judge Murphy’s ruling that allows the state to rely on organizations like the American Academy of Pediatrics, the American Academy of Family Physicians, and the American College of Obstetricians and Gynecologists – rather than the federal CDC – when establishing its childhood vaccine schedule.

This state-level movement matters for reasons beyond the immediate legal fight. It is a preview of what a child-centered policy framework looks like in practice: jurisdictions refusing to subordinate children’s health to federal dysfunction, drawing on independent scientific consensus, and building legal protections that persist regardless of what happens in Washington.

This state-level action on vaccines is part of a broader pattern worth naming:

States rejecting vaccine misinformation and promoting pro-immunization policies to protect child health.
States going beyond the federal minimum in terms of Medicaid and Children’s Health Insurance Program (CHIP) coverage levels.

And beyond health care:

States are passing far better Child Tax Credit policies than what is current law at the federal level.
States like New Mexico are passing and pursuing universal child care in light of federal failure to form a coherent national policy and recent attacks by the Administration on early childhood and child care programs.
States and voters repeatedly are rejecting school vouchers, despite the new federal policy creating tax credits to promote them.
States and schools are opposing book bans, censorship policies, and the whitewashing of curriculum, despite pressure from federal officials.
States and school districts are passing policies that eliminate school meal debt for students, despite federal policies that means-test school lunch programs.

The states that are acting and modeling what it looks like to treat the needs, concerns, and well-being of children as priorities are often doing so in the face of federal policies that are moving in the opposite direction.

Of course, there is also some disturbing backsliding at the state level that threatens the health, education, safety, and well-being of children.

South Carolina’s “Parental Rights Act” Is a Threat to Children’s Health, Safety, and Bodily Autonomy

“When evaluating the extent of parents’ legal rights, we should not merely consider how ideal parents exercise their power to provide the effective care and guidance children need. The extent of what the law enables imperfect parents to do to their children must also be taken into account… Thinking only in terms of how the best parents conduct themselves is a mistake; it is also necessary to account for what the worst parents can get away with…

9 days ago · 12 likes · Bruce Lesley

Unfortunately, states are in session right now dealing with the over $1 trillion in federal cuts to Medicaid, CHIP, and SNAP – programs designed to ensure that millions of babies and children are healthy, including providing vaccines for preventable diseases.

Furthermore, despite the positive court rulings and state legislation to continue providing vaccines to children, none of this fully erases what has already occurred, including the increased vaccine hesitancy that vaccine misinformation has spread.

Consequently, vaccination rates are falling, and children are paying the price.

The measles data alone should be cause for alarm. As CIDRAP reports:

MMR coverage among kindergartners has dropped from 95.2% in 2019–20 to 92.5% in 2024–25, leaving an estimated 286,000 kindergartners unprotected. About 92% of confirmed 2026 measles cases are among people who were unvaccinated or had unknown vaccination status.

Consequently, nearly 1,500 measles cases have been reported so far this year across 31 states, according to the CDC.

Furthermore, vaccine skepticism – fed by years of MAHA rhetoric and now amplified by federal policy – is expanding beyond vaccines into the full spectrum of routine preventive care for the youngest children.

A recent study in the Journal of the American Medical Association, which analyzed more than 5 million births nationwide, found that refusals of vitamin K shots nearly doubled between 2017 and 2024, from 2.9% to 5.2%.

That number translates into real children: at a February meeting of the Idaho chapter of the American Academy of Pediatrics, doctors said they knew of eight deaths from vitamin K deficiency bleeding in the state over the preceding 13 months.

Dr. Kristan Scott, a physician at Children’s Hospital of Philadelphia explains the danger:

Vitamin K is important for helping the blood clot and preventing dangerous bleeding in babies, like bleeding into the brain.

Dr. Paul Offit, one of the country’s foremost experts on vaccines, recently reported on a related potential disturbing rise in Haemophilus influenzae type b (Hib), a deadly form of meningitis.

At a December 2025 Florida workshop on Florida’s backsliding on vaccine mandates, Panama City pediatrician Dr. Eehab Kenawy said:

Just in the past six months, we’ve had two patients in the ICU with Hib. One child unfortunately succumbed at 4 months of age. No vaccines. One month ago, I was on call, and another patient also came into the ICU, a 2½-year-old, never vaccinated, Hib again. Abscesses in the brain, seizures, brain dead.

As Dr. Offit warns, before the Hib vaccine, the disease was the leading cause of bacterial meningitis in children under five, killing roughly 1,000 children annually. Offit’s concern: the CDC’s gutted surveillance capacity under Kennedy means we likely don’t know how many more cases like these are happening.

And still the MAHA movement wants to go further.

At a March 9 event in Washington, MAHA Institute president Mark Gorton told supporters that “the childhood vaccination schedule needs to be eliminated.”

Alongside him, Kennedy’s former communications manager Del Bigtree repeated the debunked claim that vaccines cause autism – a claim that every credible scientific body has thoroughly rejected – while showing slides arguing that measles infection reduces cancer risk. It does not.

Meanwhile, KFF polling finds that the public’s trust in CDC for providing reliable vaccine information has continued to fall, and that – by a more than 2-to-1 margin – adults who have heard about the recent changes to childhood immunizations believe it will have a negative rather than positive impact on kids.

The Administration itself reportedly knows this is a political problem. An August 2025 poll by Trump’s own pollster, FabrizioWard, found:

86% of voters believe it is important for people to receive the MMR vaccine.
85% of voters believe vaccines save lives.
90% of voters agree that “the process for approving vaccines that protect me and my family should be based on scientific evidence and should encourage, not discourage, innovation.”
89% of voters agree that “vaccine recommendations should be advised by the physicians, scientists, and public health experts trained in the medical and scientific fields that understand vaccine risks and benefits.”
82% of voters believe vaccines should be “available to all Americans at no cost.”

Judge Murphy’s ruling is important. It temporarily restores the scientific process that protects children from preventable disease. The states that have acted to insulate their vaccine schedules from federal disruption are doing something essential. These are not small things.

But they are also not sufficient. A court can restore a process. States can establish alternative schedules. Neither can undo the infections, hospitalizations, and deaths that have already occurred, the coverage gaps that have already opened, or the erosion of public trust that has taken years to develop and may take years to rebuild. Furthermore, states cannot fully replace the federal vaccine infrastructure, which ensures vaccines are ordered and safely developed across the country, due to cost and logistical constraints. States still need federal vaccine policy and federal vaccine infrastructure to operate efficiently.

The children affected by this organized abandonment of public health infrastructure did not have a vote, a lobby, or a seat at the table when these decisions were made. They never do. Even Judge Murphy’s decision focuses on the harm to physicians rather than the children themselves.

That is precisely why the rest of us – advocates, clinicians, parents, state legislators, and anyone who cares about what happens to the next generation – cannot treat a single court victory as the end of this fight.

As Sensei Sergio (Benicio Del Toro) said to Bob Ferguson (Leonardo DiCaprio) in One Battle After Another (partially filmed in El Paso, Texas, by the way):

You win some, and you lose some, Bob. Bob, Bob, Bob, get back on defense.

We must take the long game: “One Battle After Another.”

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