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Robert F. Kennedy Jr., the nominee to be the next secretary of Health and Human Services, is America’s most prominent vaccine skeptic. An advocacy organization that he founded and chaired has called the nation’s declining child-immunization rates “good news,” and referred to parents’ lingering doubts about routine shots as COVID-19’s “silver lining.” Now Kennedy may soon be overseeing the cluster of federal agencies that license and recommend vaccines, as well as the multibillion-dollar program that covers the immunization of almost half the nation’s children.

Which is to say that America’s most prominent vaccine skeptic could have the power to upend, derail, or otherwise louse up a cornerstone of public health. Raising U.S. vaccination rates to where they are today took decades of investment: In 1991, for example, just 82 percent of toddlers were getting measles shots; by 2019, that number had increased to 92 percent. The first Trump administration actually presided over the historic high point for the nation’s immunization services; now the second may be focused on promoting vaccines’ alleged hidden harms. Kennedy has said that he doesn’t want to take any shots away, but even if he were to emphasize “choice,” his leadership would be a daunting test of Americans’ commitment to vaccines.

In many ways, the situation is unprecedented: No one with Kennedy’s mix of inexperience and paranoid distrust has ever held the reins at HHS. He was trained as a lawyer and has no training in biostatistics or any other research bona fides—the sorts of qualifications you’d expect from someone credibly evaluating vaccine efficacy. But the post-pandemic era has already given rise to at least one smaller-scale experiment along these lines. In Florida, vaccine policies have been overseen since 2021 by another noted skeptic of the pharmaceutical industry, State Surgeon General Joseph Ladapo. (Kennedy has likened Ladapo to Galileo—yes, the astronomer who faced down the Roman Inquisition.) Under Ladapo’s direction, the state has aggressively resisted federal guidance on COVID-19 vaccination, and its department of health has twice advised Floridians not to get mRNA-based booster shots. “These vaccines are not appropriate for use in human beings,” Ladapo declared in January. His public-health contrarianism has also started spilling over into more routine immunization practices. Last winter, during an active measles outbreak at a Florida school, Ladapo abandoned standard practice and allowed unvaccinated children to attend class. He also seemed to make a point of not recommending measles shots for any kids who might have needed them.

Jeffrey Goldhagen, a pediatrics professor at the University of Florida and the former head of the Duval County health department, believes that this vaccine skepticism has had immense costs. “The deaths and suffering of thousands and thousands of Floridians” can be linked to Ladapo’s policies, he said, particularly regarding COVID shots. But in the years since Ladapo took office, Florida did not become an instant outlier in terms of COVID vaccination numbers, nor in terms of age-adjusted rates of death from COVID. And so far at least, the state’s performance on other immunization metrics is not far off from the rest of America’s. That doesn’t mean Florida’s numbers are good: Among the state’s kindergarteners, routine-vaccination rates have dropped from 93.3 percent for the kids who entered school in the fall of 2020 to 88.1 percent in 2023, and the rate at which kids are getting nonmedical exemptions from vaccine requirements went up from 2.7 to 4.5 percent over the same period. These changes elevate the risk of further outbreaks of measles, or of other infectious diseases that could end up killing children—but they’re not unique to Ladapo’s constituents. National statistics have been moving in the same direction. (To wit: The rate of nonmedical exemptions across the U.S. has gone up by about the same proportion as Florida’s.)

All of these disturbing trends may be tied to a growing suspicion of vaccines that was brought on during COVID and fanned by right-wing influencers. Or they could be a lingering effect of the widespread lapse in health care in 2020, during which time many young children were missing doses of vaccines. (Kids who entered public school in 2023 might still be catching up.)

In any case, other vaccination rates in Florida look pretty good. Under Ladapo, the state has actually been gaining on the nation as a whole in terms of flu shots for adults and holding its own on immunization for diphtheria, tetanus, and pertussis in toddlers. Even Ladapo’s outlandish choice last winter to allow unvaccinated kids back into a school with an active measles outbreak did not lead to any further cases of disease. In short, as I noted back in February, Ladapo’s anti-vaccine activism has had few, if any, clear effects. (Ladapo did not respond when I reached out to ask why his policies might have failed to sabotage the state’s vaccination rates.)

  

If Florida’s immunization rates have been resilient, then America’s may hold up even better in the years to come. That’s because the most important vaccine policies are made at the state and local levels, Rupali Limaye, a professor and scholar of health behavior at Johns Hopkins University, told me. Each state decides whether and how to mandate vaccines to school-age children, or during a pandemic. The states and localities are then responsible for giving out (or choosing not to give out) whichever vaccines are recommended, and sometimes paid for, by the federal government.  

But the existence of vaccine-skeptical leadership in Washington, and throughout the Republican Party, could still end up putting pressure on local decision makers, she continued, and could encourage policies that support parental choice at the expense of maximizing immunization rates. As a member of the Cabinet, Kennedy would also have a platform that he’s never had before, from which he can continue to spread untruths about vaccines. “If you start to give people more of a choice, and they are exposed to disinformation and misinformation, then there is that propensity of people to make decisions that are not based on evidence,” Limaye said. (According to The New York Times, many experts say they “worry most” about this aspect of Kennedy’s leadership.)

How much will this really matter, though? The mere prominence of Kennedy’s ideas may not do much to drive down vaccination rates on its own. Noel Brewer, a behavioral scientist and public-health professor at the UNC Gillings School of Global Public Health, told me that attempts to change people’s thoughts and feelings about vaccines are often futile; research shows that talking up the value of getting shots has little impact on behavior. By the same token, one might reasonably expect that talking down the value of vaccines (as Kennedy and Ladapo are wont to do) would be wasted effort too. “It may be that having a public figure talking about this has little effect,” Brewer said.

Indeed, much has been made of Kennedy’s apparent intervention during the 2019 measles crisis in Samoa. He arrived there for a visit in the middle of that year, not long after measles immunizations had been suspended, and children’s immunization rates had plummeted. (The crisis began when two babies died from a vaccine-related medical error in 2018.) Kennedy has been linked to the deadly measles outbreak in the months that followed, but if his presence really did give succor to the local anti-vaccine movement, that movement’s broader aims were frustrated: The government declared a state of emergency that fall, and soon the measles-vaccination rate had more than doubled.

As head of HHS, though, Kennedy would have direct control over the federal programs that do the sort of work that has been necessary in Samoa, and provide access to vaccines to those who need them most. For example, he’d oversee the agencies that pay for and administer Vaccines for Children, which distributes shots to children in every state. All the experts I spoke with warned that interference with this program could have serious consequences. Other potential actions, such as demanding further safety studies of vaccines and evidence reviews, could slow down decision making and delay the introduction of new vaccines.

Kennedy would also have a chance to influence the nation’s vaccine requirements for children, as well as its safety-and-monitoring system, at the highest levels. He’d be in charge of selecting members for the Advisory Committee on Immunization Practices, which makes recommendations on vaccines that are usually adopted by the states and result in standardized insurance coverage. He’d also oversee the head of the CDC, who in turn has the authority to overrule or amend individual ACIP recommendations.

Even if he’s not inclined to squelch any determinations outright, Kennedy’s goal of giving parents latitude might play out in other ways. Brewer, who is currently a voting member of ACIP (but emphasized that he was not speaking in that capacity), said that the committee can issue several different types of rulings, some of which roughly correspond to ACIP saying that Americans should rather than may get a certain vaccine. That distinction can be very consequential, Brewer said: Shots that are made “routine” by ACIP get prioritized in doctor’s offices, for instance, while those that are subject to “shared clinical decision-making” may be held for patients who ask for them specifically. Shifting the country’s vaccination program from a should to a may regime “would destroy uptake,” Brewer told me.

Those would seem to be the stakes. The case study of vaccine-skeptical governance that we have in Florida may not look so dire—at least in the specifics. But Kennedy’s ascendancy could be something more than that: He could steer the public-health establishment off the course that it’s been on for many years, and getting back to where we are today could take more years still.

The reelection of Donald Trump might seem like doomsday for America’s public-health agencies. The president-elect has vowed to dismantle the federal bureaucracy.Robert F. Kennedy Jr., potentially his next health czar, wants to go even further. As part of his effort to “Make America healthy again,” Kennedy has recently promised to tear up the FDA and its regulations, including those governing vaccines and raw milk. But that effort is going to run into a major roadblock: the “deep state.”

The phrase deep state might trigger images of tinfoil hats. After all, Trump has spent much of the past eight years falsely claiming that Democratic bureaucrats are unfairly persecuting him. But operating within the federal health agencies is an actual deep state, albeit a much more benign and rational one than what Trump has talked about. And he might not be able to easily tear it down.

Whether you know it or not, you’ve likely seen this deep state in action. It was the reason Trump’s preferred treatment for COVID during the early phases of the pandemic, hydroxychloroquine, was not flooding pharmacies. And it was why COVID vaccines were not rushed out before the 2020 presidential election. Both of those efforts were stopped by civil servants, despite overt pressure from Trump and officials in his administration.

Public-health officials didn’t buck Trump to sabotage him. They did so because both measures were scientifically unsolid. Vaccines weren’t authorized before the election because FDA officials knew that they had to wait at least two months after the clinical trials were completed to make sure the vaccines didn’t cause dangerous side effects. And the FDA blocked use of hydroxychloroquine for treating COVID because of the drug’s unproven efficacy and spotty safety record.

If they really wanted to, health officials could have caved to Trump’s requests. But in general, they don’t easily renounce their empirically grounded views on science—regardless of who is president. The FDA’s top vaccine regulator vowed to resign in 2020 if the agency relented to Trump’s pressure to approve vaccines early. Two other vaccine regulators resigned in the first year of the Biden administration after the FDA announced the rollout of COVID boosters. Following their resignations, the ex-officials publicly argued that “the data simply does not show that every healthy adult should get a booster,” and that public-health efforts should have been entirely focused on “vaccinating the unvaccinated, wherever they live.”

Many scientists, lawyers, and doctors are involved in each and every decision that federal-health agencies make, because the decisions must be evidence-based. Arbitrary decisions based on conspiracy theories or political whims can, and will, be challenged in court. “A new administration absolutely can come in and set new policies,” Lowell Schiller, who led the FDA’s office of policy during part of Trump’s first term, told me. But, he added, “there is a lot of law that they need to follow, and things have to be done through proper process.”

Some changes that may seem relatively insignificant require reams of paperwork. When the FDA wanted to revoke the standardized federal definition of frozen cherry pie (yes, one existed until earlier this year), it had to go through a formal procedure that forced the agency to defend its legal authority to make the move as well as the costs and benefits of a more laissez-faire cherry-pie policy. The process took more than three years. Few things are harder than approving or revoking approval for a drug: In 2020, the FDA tried to pull an unproven drug meant to prevent preterm births. Despite lots of evidence that the drug was ineffective, the process took nearly three years. Now imagine how things would go if RFK Jr. pressured the FDA to pull a vaccine off the market because he is convinced, incorrectly, that it causes autism.

A Trump administration could do a few things more easily. It could, for example, direct the FDA to stop enforcing the agency’s restrictions on some of the products that Kennedy touts, such as raw milk and certain vitamins. The FDA often declines to go after various products in the name of “enforcement discretion.” A downturn in enforcement actions might anger some within the agency, but Trump could bring that about with little red tape.

Kennedy has promised mass firings at the FDA, presumably to install loyalists who would enact the agenda. That threat should be taken seriously. The president has sweeping power to hinder officials who muck up his agenda. The Trump administration allegedly demoted one top federal official who pushed back against authorizing hydroxychloroquine.

But there are major checks, too, on what a president can do to turn the screws on civil servants. Unlike many workers, federal employees can be fired only for cause or misconduct, and civil servants are entitled to appeals in both cases. “It’s a tangled process that makes it hard to be able to get rid of people,” Donald Kettl, an emeritus public-policy professor at the University of Maryland, told me. Trump was famous for firing people during his first term, but the people who got the axe were political appointees who did not have the same protections as civil servants. In short, few federal employees last just one Scaramucci.

However, one major threat still looms over federal workers. In his first term, Trump pursued an effort to reclassify federal workers in a way that would strip many of them of their protections, and he has said that in his second term he will “immediately” pursue that action. Trump would have to go through an arduous process to make good on that threat, and it would likely be challenged in court. But if implemented, the policy could give Trump massive leverage to fire workers.

Still, Trump takes those actions at the peril of his own agenda. The reality is that the same members of the so-called deep state that Trump and Kennedy are threatening to fire are also essential to making anything the administration wants to do happen. Seminal parts of the “Make America healthy again” agenda would have to run through this deep state. If Kennedy, a champion of psychedelics, wants the FDA to approve a new psilocybin-based treatment, the medicine must be reviewed by the scientists and doctors who review other drugs for safety and efficacy. If he wants a national ban on fluoride in water, that must go through the EPA. There is no way around this: Even if Trump appointed Kennedy as the unilateral king of every single federal health agency, Kennedy cannot make these decisions on his own.

A central tenet of the “Make America healthy again” agenda is removing potentially dangerous chemicals from food. Although the FDA has been slow to ban certain chemical additives, the agency seems to have recently seen the light. Earlier this year it set up a new initiative for reassessing the safety of these substances. But if Kennedy guts the FDA, no one might be there to do that review.

The Trump administration could hypothetically hold a massive job fair to get cronies into all of those roles—especially if the president-elect makes good on his promise to make hiring and firing bureaucrats easier—but few people can successfully perform these highly technical jobs, not to mention that hiring in the federal government typically takes forever. (The average hiring time in 2023 was 101 days.)

Still, Trump’s second term will be one of the biggest challenges facing our federal health system. No president in modern history has been so intent on bending health agencies to his will, and he seems even more emboldened to do so now than in his first go-around. Trump will likely have some successes—some people may be fired, and some important policies may be scrapped. America is about to find out just how resilient the deep state really is.