Kennedy’s most high-profile battlefield has always been vaccines.

Last June, just four months into his term, Kennedy struck down the decades-old Advisory Committee on Immunization Practices (ACIP). He fired all 17 members, replacing them with a slate of vaccine skeptics and even promoters of misinformation.

More shockingly, then-CDC Director Rochelle Walensky was soon dismissed by Kennedy for refusing to lay off senior staff and reject recommendations from his handpicked vaccine panel.

Insiders fear these moves have effectively gutted America’s scientific decision-making system for vaccines.

In December, fears were fully realized: the newly reconstituted ACIP quickly reversed nearly three decades of policy, dropping the universal recommendation that newborns receive the hepatitis B vaccine within 24 hours of birth.

In January, the CDC issued a medically explosive “decision memo.” Without presenting any new scientific evidence, it removed seven childhood vaccines—including rotavirus, hepatitis A, and influenza—from the “universally recommended” list, downgrading them to “shared clinical decision-making.” This means the U.S. government no longer explicitly endorses these vaccines as necessary for all children.

The decision triggered a legal and political “tsunami.”

A bipartisan coalition of 15 states swiftly sued, accusing Kennedy of “bypassing federal law, ignoring scientific evidence, and endangering children’s health.”

Leading medical groups such as the American Academy of Pediatrics decried in court that this posed “a clear and present danger to public health.” For the more than 100 million Americans without regular access to primary care, they argued, “discussing with a doctor” is not a neutral suggestion—it is a tangible barrier to vaccination.

In February, the FDA rejected Moderna’s application for a new mRNA influenza vaccine, a move widely seen as Kennedy’s camp “showing its teeth” to the vaccine industry.

Yet, inexplicably, the review was reinstated weeks later without any scientific explanation. The reversal left Kennedy’s most fervent anti-vaccine base confused and angry. In their eyes, the “holy war leader” they had elevated to power had betrayed the movement’s original goals.

Why are COVID-19 vaccines still being administered to millions of children? Why do pharmaceutical giants remain protected by law? As Kennedy avoided vaccine issues on his national tour ahead of the midterm elections, radicals felt profound disillusionment.

One anti-vaccine activist from Texas interviewed by The New York Times said he thought he had finally found a politician who would end corporate pharmaceutical power—only to discover it was a facade. In retaliation, threats have emerged that the “medical freedom movement” will abandon the GOP in the midterms if the mRNA flu vaccine is approved.

This sense of “betrayal” encapsulates Kennedy’s dilemma: he is walking a tightrope between reshaping the public health system and preserving his political alliances, only to find trust eroding on both sides.

If the swings in vaccine policy were political theater, the chaos inside the FDA represents a staggering systemic challenge.

For a long time, the FDA was regarded as the “gold standard” of pharmaceutical regulation. Yet over the past year, the agency has undergone a complete collapse in leadership: within the Center for Drug Evaluation and Research (CDER) alone, five directors have been replaced in a single year.

The personnel upheaval stems partly from Kennedy’s purge of professional staff, and partly from the controversial “National Priority Review Voucher” program pushed by his handpicked FDA Commissioner Marty Makary. The plan seeks to use political pressure to speed up approvals for certain drugs in exchange for corporate pricing commitments.

But insiders have slammed the approach for placing scientific decisions amid “anxiety, fear, and confusion.”

According to the Associated Press, multiple senior FDA officials resigned rather than sign legal documents, fearing that politically driven fast-track approvals—rather than science—would expose both the agency and themselves to future legal risk.

Even more alarming: scientists have been stripped of their authority. Under the FDA’s new model, final review decisions no longer rest with the scientific reviewers who know the data best, but are voted on by committees of senior officials—upending decades of FDA tradition.

Chaos has also unfolded at CBER, once led by Prasad.

An epidemiologist known in academic circles for fierce criticism of the FDA, Prasad ruled with an iron fist upon taking office. He repeatedly overturned the conclusions of subordinate reviewers and set extremely high approval bars for rare disease drugs.

In February, Prasad rejected Regenxbio’s gene therapy RGX-121 and Disc Medicine’s bitopertin for erythropoietic protoporphyria, largely over objections to approvals based on biomarker surrogates instead of clinical placebo-controlled trials.

In March, the FDA issued a Complete Response Letter (CRL) to uniQure, requiring large-scale late-stage controlled trials for its Huntington’s disease gene therapy rather than approval via the accelerated pathway. The decision sent uniQure’s stock plummeting 33% in a single day.

Prasad’s style created a “chilling effect” among investors.

Data shows that under his tenure, the number of accelerated approvals at the FDA plunged from 20 in the Biden-era 2024 to just 9 in 2025. Investors began shunning small biotech companies reliant on early-stage data.

Though Makary tried to defend Prasad as a “genius” under a “media witch hunt,” the market ultimately delivered its verdict.

On March 7, news broke that Prasad would step down and return to academia. uniQure’s stock surged as much as 70% in after-hours trading, with Regenxbio jumping 29%. The dramatic rally reflected the biotech industry’s relief at the official’s departure—and a silent indictment of the FDA’s unpredictability over the past year.

Kennedy’s destruction has spread like a virus through the entire HHS apparatus, eroding the foundation of U.S. scientific research and disease control.

At the NIH, hailed as the “crown jewel” of federal research, the brain drain is staggering. An analysis by Science found that more than 2,400 PhD-level employees left the NIH, CDC, and FDA last year—two to three times the number in 2024.

Over half of the NIH’s 27 institutes lack permanent directors. This leadership vacuum has directly translated to shrinking research funding. Compared with 2024, the NIH awarded roughly 24% fewer new grants to academic labs.

Meanwhile, a Nature assessment found that researchers funded by the NIH and the National Science Foundation have lost roughly $1.4 billion amid relentless funding cuts and court battles to restore them. Behind these numbers lie countless interrupted clinical trials and the erosion of America’s life sciences discovery potential for decades to come.

The CDC’s situation resembles a slow “euthanasia.”

NIH Director Jay Bhattacharya is temporarily serving as acting CDC head. Before him, the agency saw Rochelle Walensky fired after just four weeks, HHS Deputy Secretary Jim O’Neill as a brief placeholder, and second-in-command Ralph Abraham resigning suddenly after only three months citing “unforeseen family matters.”

A top public health agency with decades of history has been reduced to the absurdity of having no permanent leadership.

The lack of command has paralyzed core functions. In January, an analysis in Annals of Internal Medicine found that many key data series traditionally published regularly by the CDC are either severely delayed or no longer released at all. Over the past year, the agency has issued only a handful of health alerts, compared with dozens in a normal year.

This top-down erosion of professional authority is having irreversible consequences. As Kennedy encourages the public to “do their own research” and scientific decisions are replaced by political loyalty, public trust in the public health system collapses like a house of sand.

Some states and medical associations have begun to save themselves, forming their own public health alliances to coordinate resources and release evidence-based information during outbreaks. What began as temporary patches have now evolved into powerful alternative forces.

The question remains whether these fragmented efforts can fill the vacuum left by the CDC. Even more worrying, Kennedy has set his sights on a new target: the National Vaccine Injury Compensation Program.

Recently, Kennedy fired half the panel of experts responsible for determining payouts. Critics fear that if his appointees push to expand coverage to include scientifically unsubstantiated harms—such as autism—the fund will quickly be depleted, and drugmakers will halt vaccine production rather than bear unbearable litigation risks.

A year ago, when Kennedy took control of HHS, his supporters saw a hero breaking the system, while his opponents foresaw a scientific catastrophe. A year later, the brutal reality has exceeded all expectations.

The young man who once nearly died from a drug overdose on a plane has, after redemption, fame, and ultimate power, pushed the nation’s health into an unknown, still-unfolding abyss: measles has returned, research funding is broken, regulation is unpredictable, and top talent has scattered.

Perhaps The Lancet was not exaggerating. The turmoil Kennedy has unleashed in one year will take generations to repair.