And froze the federal government’s ability to change any vaccine recommendation in the process.

Something happened on March 16 that Kennedy’s people need to understand.

District Judge Brian Murphy in Massachusetts issued a preliminary injunction in AAP v. Kennedy that freezes the federal childhood vaccine schedule and strips the CDC Director of the authority to change who gets which vaccines. Not for a week. Not until the next hearing. For the duration of this case, which could be years.

Let me explain what he actually did, because I don’t think the people advising Kennedy understand it.

THE TWO HOLDINGS THAT SHUT EVERYTHING DOWN

The court’s order does two things. First, he held that the CDC Director cannot change the immunization schedule without ACIP origination. Then Acting Director Jim O’Neill’s January 5, 2026 decision was invalid, Murphy ruled, because it didn’t come through ACIP. The Director can’t initiate. He can only accept or reject what ACIP gives him. (Opinion at 21: “the CDC cannot simply bypass ACIP in altering the immunization schedules.”)

Second, it stayed the appointments of all thirteen ACIP members he found were improperly appointed. (Opinion at 43-44.) He found Kennedy violated “balance” requirements. ACIP cannot meet. Cannot deliberate. Cannot vote.

Read those two holdings together. The Director can’t act because the Court says only ACIP can originate. ACIP can’t act because the Court shut it down.

Here is the Court’s opinion. PI order

I’ll say it plainly: the CDC Director cannot, right now, today, change a single vaccine recommendation on the childhood schedule. Cannot reclassify a vaccine. Cannot act on new safety data about an existing vaccine. Cannot recommend a new vaccine the FDA authorizes. The CDC’s scientists can still track diseases, run laboratories, investigate outbreaks. What they cannot do is watch their Director act on their work. If the science changes on any of the seventeen currently recommended vaccines, the Director can’t respond. If the FDA authorizes a new vaccine tomorrow, the Director can’t recommend it. The recommendation apparatus is frozen, and it stays frozen until this case is resolved or ACIP is reconstituted to Murphy’s satisfaction.

HERE IS WHAT THE COURT HAS PARALYZED

The CDC employs approximately 13,000 people, or about 10,000 after the 2025 cuts took a quarter of the workforce. Sixty percent hold master’s degrees or doctorates: epidemiologists, virologists, immunologists, microbiologists, physicians, veterinarians, statisticians, and laboratory scientists. The agency’s budget is $9.2 billion. (USAFacts, Sept. 2024; PBS, Feb. 2025; NPR, Oct. 2025.)

The CDC operates three entire national centers devoted to infectious disease. Three. Not departments. National centers. (USGovernmentManual.gov.)

The first is the National Center for Immunization and Respiratory Diseases, NCIRD. This is the one that matters here, because it directly manages the childhood immunization schedule, runs the Vaccines for Children program, and staffs ACIP’s own meetings. It reports to the Deputy Director for Infectious Diseases, who reports to the CDC Director, who reports to the HHS Secretary. (CDC.gov, NCIRD Organizational Chart, approved July 17, 2024; Federal Register, 89 FR 59101, July 22, 2024.)

Five divisions. Twenty-three branches. Here’s what Judge Murphy says can’t initiate a vaccine recommendation:

The Immunization Services Division alone has eight branches. It manages the national vaccine supply chain, tracks every vaccine administered in America, monitors every vaccine-preventable disease in the country, conducts applied research on vaccine effectiveness, and deploys field epidemiologists to health departments across all fifty states. It also prepares the evidence packages ACIP reviews and staffs ACIP’s meetings. Let that sink in. The division that does the work, that builds the scientific record, that briefs the committee, needs permission from the fifteen part-timers it briefs. Under Murphy’s framework, the people who prepare the briefing books need permission from the people who read them.

The Influenza Division has four branches: virology, epidemiology, immunology, and global influenza. These are the scientists who track flu variants worldwide and develop the annual vaccine composition recommendations. If a new flu strain emerges next winter, they’ll have the data, the analysis, and the recommendation ready. And it will sit on a shelf, because the Director can’t act on it without permission from a committee that can’t meet.

The Division of Viral Diseases has three branches covering polio, measles, mumps, rubella, varicella, rotavirus, and norovirus.

The Division of Bacterial Diseases has four branches: two epidemiology branches and two reference laboratories covering pneumonia, streptococcus, meningitis, pertussis, and diphtheria. The laboratories that diagnose these diseases for the entire country are housed in this division.

The Coronavirus and Other Respiratory Diseases Division has four more branches: laboratory, surveillance, epidemiology, and global operations. Created because of COVID, now frozen along with everything else.

That’s one center. The second center, NCEZID, has seven more divisions, with operations in Atlanta, Fort Collins, Colorado, San Juan, Puerto Rico, and Anchorage, Alaska, plus quarantine facilities in twenty cities across the country. (CDC.gov, NCEZID Divisions and Offices.) The third center covers HIV/AIDS, Viral Hepatitis, STD, and TB Prevention.

All of it reports up through the CDC Director. These divisions can still do their science: track pathogens, run reference labs, deploy field epidemiologists, monitor disease. What Judge Murphy says the Director cannot do is act on any of it to change a vaccine recommendation. The surveillance systems keep running. The data keeps flowing. And the Director sits on it, because under Murphy’s framework, only ACIP can originate a change to who gets which vaccine. They all have to wait for fifteen part-time Special Government Employees under 18 U.S.C. § 202(a) who meet three times a year.

And the Court stayed their appointments. So, there is nobody to wait for.

One preliminary injunction, entered at the request of seven medical trade organizations has done what no pathogen, no budget crisis, and no prior administration has done: taken the federal government out of the vaccine recommendation business.

WHY THE COURT IS WRONG ON THE LAW

Judge Murphy’s ACIP-origination requirement doesn’t exist in any statute. It appears nowhere in the text.

The Federal Advisory Committee Act says advisory committees exist “solely for advisory functions” and that determinations of policy “shall be made solely by the President or an officer of the Federal Government.” 5 U.S.C. § 1008(b). ACIP advises. The Director decides. CDC’s own ACIP Policies and Procedures confirm it: the Director “may adopt or reject” ACIP recommendations, with a structured disagreement pathway including internal decision memos and Federal Register notice. The Supreme Court recognized this in Braidwood Management v. Kennedy, where footnote 4 acknowledges the Director’s discretion in “adopting” ACIP recommendations. “Adopting” presupposes independent authority. You don’t “adopt” something if you’re required to accept it.

No case has ever held that the CDC Director is required to consult with ACIP before issuing vaccine recommendations. In the entire history of the CDC. This is the first. The order imposes a precondition the text does not contain, and then shuts down the only body the order says the Director needs.

WHAT FORMER ACTING DIRECTOR O’NEILL ACTUALLY DID

Nobody seems to be talking about what the January 5 decision actually said. The hysteria has been about Kennedy. The legal briefs have been about process. So here’s the substance.

O’Neill’s decision was based on analyses from the NIH, the FDA, and scientific experts across federal agencies. (Opinion at 10.) The HHS assessment found that the United States was “a global outlier among peer nations,” recommending more childhood vaccines than any peer nation and more than twice as many doses as some European countries. The U.S. didn’t have better outcomes to show for it. I covered this in detail in my earlier piece on the Denmark schedule hysteria, but the short version: seventeen EU nations, the UK, and Japan use shared clinical decision-making with vaccination rates equal to or higher than ours. The outlier is us.

O’Neill’s decision kept eleven vaccines recommended for all children. It moved six to either high-risk or shared clinical decision-making. No vaccine was eliminated. No vaccine was made illegal. No insurance coverage changed.

Massachusetts, where AAP filed this case, requires immunization against nine diseases for school entry. California requires ten. O’Neill recommended eleven. AAP called this “a very dark day for children” but has never sued Massachusetts or California for requiring fewer vaccines than AAP wants. Funny how that works.

Judge Murphy restored a schedule that exceeds what every state in the country actually mandates. Including his own.

THE UPSELL

Here’s what this is really about.

No state in the union mandates immunization against seventeen or eighteen diseases. Massachusetts mandates 10, as does California. Every pediatrician in America who follows the pre-Kennedy CDC schedule was already recommending more vaccines than their state requires for school entry. That has always been the case. AAP’s entire business model depends on persuading parents to accept vaccines beyond what state law requires. That’s the upsell. And it has always required a sales pitch, because the states, which actually have the constitutional authority to mandate vaccines, looked at these diseases and decided not to require vaccination against all of them.

Judge Murphy’s order doesn’t protect children. It restores a federal recommendation that gives AAP a stronger platform to promote vaccine uptake beyond what any state legislature has determined is necessary to protect children.

Preliminary injunctions are supposed to preserve the status quo pending litigation. This one hands a trade association a marketing tool.

THE COVID ABSURDITY

The Court’s stay restores universal COVID-19 recommendation for healthy children. (Opinion at 42-44.) No COVID-19 vaccine is approved or authorized for healthy children at any age in the United States. The FDA limited approval to high-risk children only. The CBER Director wrote that the benefit-risk standard “is not met” for healthy children.

AAP’s own members had already stopped stocking the vaccine. AAP’s former committee chair told AAP News that pediatricians “have not been stocking it for quite some time now, because the demand is low and the cost is high.” VFC itself stopped requiring providers to stock COVID vaccines in July 2025.

So the Court restored a recommendation that the FDA rejected, that AAP’s own members abandoned, and that the VFC program stopped enforcing. And here’s the part that should make everyone uncomfortable: the restored recommendation is enforced through VFC, which binds only doctors serving Medicaid children. Private-practice pediatricians can ignore it. They already were ignoring it. Medicaid doctors cannot. Informed consent for families who can afford a private pediatrician. Compelled compliance for families who can’t. That’s what seven trade organizations and one federal judge call protecting children.

AAP HAS TAKEN OVER THE GOVERNMENT’S ROLE

AAP published its own “Harmonized Schedule” after the January 5 revision. It told its 67,000 members to keep vaccinating exactly as before. Its Committee on Infectious Diseases chair told pediatricians at a webinar: “You all create the trust with the patient, not the federal government.” A chapter VP told doctors to proceed as usual and not even mention the CDC’s changes unless a parent brought it up.

AAP’s medical guidance didn’t change. Its members’ practices didn’t change. The vaccines didn’t disappear. The insurance coverage didn’t change. AAP was already conducting a nationwide campaign to maintain vaccine uptake at levels no state legislature has mandated. What it wanted from Murphy was a federal court order to make that campaign easier. “Ignore the CDC” is a harder sell to a hesitant parent than “the CDC agrees with us because a federal judge said so.” That’s what Judge Murphy gave them. A taxpayer-funded marketing tool for seven trade organizations’ vaccine promotion campaign that goes beyond what every state in the country requires.

THE GOVERNMENT HAS TO APPEAL

If Kennedy’s advisors are telling him there’s nothing to do about Judge Murphy’s order and that the solution is to just to reconstitute the ACIP committee, then his advisors are terribly wrong.

One district judge in Massachusetts has issued an order that, as a practical matter, eliminates the federal government’s capacity to make vaccine policy. Not delays it. Not modifies it. Eliminates it. The Director can’t act because Judge Murphy says only ACIP can originate. ACIP can’t act because he enjoined most ACIP appointments. If a novel pathogen emerges tomorrow, if there’s a measles outbreak in a school district next week, the federal government has no committee, no director, and no secretary with the authority under the Court’s framework to respond. The public health infrastructure of the United States is frozen by a single preliminary injunction issued on the application of seven trade organizations whose members sell vaccines.

And this isn’t an academic separation-of-powers puzzle. This is operational. The government cannot convene its vaccine advisory body. The government’s chief health officers cannot act independently. The apparatus Congress built over sixty years is offline. One judge did that. And he did it on a record where the other side of the argument was never presented because the only parties who would have presented it were denied intervention in one sentence.

A single district judge has shut down federal vaccine policy in the United States. The March 16 order holds that vaccine policy must originate in the Advisory Committee on Immunization Practices. The same order stays the appointments of all thirteen ACIP members and prohibits the committee from meeting. The Director cannot act because Murphy says only ACIP can originate. ACIP cannot act because Murphy enjoined it. If a novel pathogen emerges tomorrow, the federal government has no committee to convene, no director authorized to act, and no secretary empowered to respond. That condition persists for the duration of this litigation. One preliminary injunction, entered at the request of seven medical trade organizations, has frozen the public health infrastructure Congress built over sixty years.

The government argued its actions were unreviewable and lost on every issue. It never challenged the statutory framework Murphy adopted. Appellants moved to intervene to present that challenge. They filed three declarations, twenty exhibits, and a 30-page set of Proposed Findings demonstrating the preliminary injunction should be denied on every Winter factor. The district court denied intervention in one sentence. The amicus brief raising these arguments was dismissed in a footnote. Murphy then adopted a reading of the statute that no party contested and no adversarial process tested.

FACA’s ‘fairly balanced’ requirement is an example of that exception.

The Ninth Circuit held it is ‘a political question that is best left to the other branches of government.’ Center for Policy Analysis on Trade and Health v. Office of U.S. Trade Representative, 540 F.3d 940, 945 (9th Cir. 2008). Judge Silberman wrote in the D.C. Circuit that ‘the relevant points of view on issues to be considered by an advisory committee are virtually infinite and, therefore, the judgment as to what constitutes an appropriate or fair balance of those views must be a political one.’ Public Citizen v. National Advisory Committee on Microbiological Criteria for Foods, 886 F.2d 419, 426-30 (D.C. Cir. 1989).

Judge Murphy reviewed something courts have said is unreviewable, applied a standard he never defined, and stayed every appointment the Secretary made. Any new appointments Kennedy makes will have to satisfy whatever ‘balance’ criteria Judge Murphy has in mind, criteria no court has been able to define because the statute provides no standard to define them by. That is judicial control of executive branch staffing.

It’s worth noting that AAP didn’t challenge the three ACIP members who voted for universal recommendation at every meeting. AAP had no objection to their ‘balance.’ The only members AAP found insufficiently balanced were the ones who voted for shared clinical decision-making, the same approach seventeen EU nations, the UK, and Japan use. Under AAP’s theory, ‘balanced’ means ‘agrees with AAP.’ That’s a loyalty test, which ironically, AAP indirectly accused Kennedy of employing.

And even if ACIP reconvenes, Judge Murphy’s framework means any future vaccine action the CDC takes that AAP doesn’t like produces the same result. Another amended complaint. Another PI motion. Or depending on what the CDC decides to change, a contempt motion. This decision makes the CDC unable to act or react on vaccine policy regardless of what evidence turns up, what pathogens emerge, or what the science shows, because every action that doesn’t originate in an ACIP that meets the court’s undefined standards is subject to the same or new preliminary injunction.

THE GOVERNMENT HAS TO APPEAL THIS ORDER.

Forget the politics of the schedule revision. Judge Murphy’s legal framework, if it stands, means no CDC Director, no HHS Secretary, and no future administration can change a vaccine recommendation without first getting permission from a part-time advisory committee. If new evidence emerges about any vaccine on the schedule, the Director can’t act on it. If the FDA authorizes a new vaccine, the Director can’t recommend it. Congress created ACIP to advise. FACA says so. Every federal agency operates that way. Murphy turned it upside down.

The practical effect of this order is that one federal district court judge (so far, and for now anyway) OVERSEES federal vaccine policymaking. The Secretary must seek judicial approval before appointing advisory committee members. The new Acting CDC Director, Jay Bhattacharya, must demonstrate to the Court’s satisfaction that he has sufficiently ‘consulted’ with ACIP members whose appointments the court has approved. Courts have recognized, as shown above, that the composition of federal advisory committees is committed to executive discretion and is not reviewable. Judge Murphy’s order converts that discretion into a judicial gatekeeping function.

The head of the two largest public health agencies in the federal government needs a district judge’s permission to staff his own advisory committee and act on his own public health authority. That is not what FACA contemplates. It is not what separation of powers permits.

WHAT THIS IS REALLY ABOUT

Right now, seven trade organizations via a district judge have more control over federal vaccine policy than the CDC Director, the HHS Secretary, and 10,000 federal scientists combined. They got it from a district court who invented a legal requirement that doesn’t exist in any statute, applied it retroactively, and then shut down the only body he said can satisfy it.

We moved to intervene in the case on behalf of two mothers whose children died after receiving the schedule AAP wants restored, two doctors who lost their licenses for deviating from it, and Children’s Health Defense. We filed three declarations, twenty exhibits, and a 30-page set of Proposed Findings demonstrating the PI should have been denied on every Winter factor.

We presented the evidence no one else would present. The Institute of Medicine found in 2002 and again in 2013 that the cumulative childhood immunization schedule has never been tested for safety. AAP’s complaint says it was “rigorously tested.” The IOM says it wasn’t. Neither the government nor AAP cited the IOM reports. Nobody in the courtroom told the judge. Murphy accepted “rigorously tested” without challenge and built his entire merits analysis on it. (Opinion at 43 n.75, dismissing our evidence in a footnote.)

Judge Murphy denied intervention in one sentence. (Dkt. 271, Feb. 27, 2026.) No analysis. No findings. The same form language he used to deny a pro se individual, applied without modification to five represented parties with dead children, revoked licenses, and a pending RICO action. One sentence.

We intend to file an emergency motion under FRAP 8 in the First Circuit seeking reversal of the intervention denial, party status in the appeal, and a stay of Murphy’s PI.

The government argued only that its actions were unreviewable. That’s why it lost on every issue. (Opinion at 20-22.) It never challenged Murphy’s statutory framework. It never presented the scientific case for the schedule revision. It never cited the IOM reports. It never identified a child harmed under the prior schedule. We did. And we were thrown out in one sentence.

We’re going back in. The First Circuit can reverse Murphy’s intervention denial, grant us party status, and stay the PI. We intend to make every argument the government failed to make and present every piece of evidence the government failed to present. Hopefully the government will join us this time. Because someone in that courtroom needs to tell the First Circuit what FACA actually says, what the CDC Director’s authority actually is, and what Murphy’s order actually does to the federal government’s ability to protect the public from infectious disease.

The country moved on. The states moved on. Seventeen nations that use the model AAP calls dangerous vaccinate at rates equal to or higher than the United States. The families whose children died under the schedule AAP wants restored moved on, too, to a RICO courtroom in Washington.

The only people who haven’t moved on are seven trade organizations and one district judge. They think a preliminary injunction can put seven vaccine uptake trade organizations in charge of vaccine policy for 330 million Americans.

We think otherwise.

Rick Jaffe, Esq.

Postscript

Connecticut’s DPH Commissioner Manisha Juthani applauded Judge Murphy’s order, telling NBC Connecticut: “We have not changed our schedule. The schedule is exactly the same. We do not have any intention to change anything.”

Connecticut mandates eight childhood vaccines. Conn. Gen. Stat. § 10-204a. The schedule she’s applauding recommends seventeen. You don’t see her arguing Connecticut should mandate the other nine. These other vaccines are essential enough to justify a federal injunction but not so essential for Hartford to require them. Seven trade groups that couldn’t convince the Connecticut General Assembly convinced a Boston federal judge to do what Hartford wouldn’t: help upsell vaccines no state thinks are necessary.

Sources

CDC organizational structure, NCIRD: CDC.gov, “National Center for Immunization and Respiratory Diseases (NCIRD),” NCIRD Organizational Chart, approved July 17, 2024, https://www.cdc.gov/about/divisions-offices/ncird.html

NCIRD reorganization and branch-level detail: Federal Register, 89 FR 59101 (July 22, 2024), https://www.federalregister.gov/documents/2024/07/22/2024-16027/reorganization-of-the-national-center-for-immunization-and-respiratory-diseases

NCEZID organizational structure and locations: CDC.gov, “NCEZID Divisions and Offices,” https://www.cdc.gov/ncezid/divisions-offices/index.html
CDC three infectious disease centers: USGovernmentManual.gov, Centers for Disease Control and Prevention, https://www.usgovernmentmanual.gov/Agency?EntityId=pG2OjWAiFrE%3D

CDC workforce size (pre-cuts): USAFacts (Sept. 2024 data: 12,820 civilian employees), https://usafacts.org/explainers/what-does-the-us-government-do/subagency/centers-for-disease-control-and-prevention/

CDC workforce qualifications: PBS NewsHour (Feb. 14, 2025) (“about 13,000 employees”; “60 percent have master’s degrees or doctorates”), https://www.pbs.org/newshour/politics/cdc-set-to-lose-one-tenth-of-workforce-under-trump-administration-probationary-job-cuts

CDC workforce cuts: NPR (Oct. 16, 2025) (“CDC has lost around 3,000 employees”; “down by around 33% of their staff since January”), https://www.npr.org/2025/10/14/nx-s1-5574469/cdc-shutdown-federal-layoffs

CDC budget: PBS NewsHour (Feb. 14, 2025) (“$9.2 billion core budget”)

Murphy opinion: AAP v. Kennedy, No. 1:25-cv-11916-BEM (D. Mass.), Dkt. 291 (Mar. 16, 2026)