In a dramatic and contentious turn for U.S. public health policy, Health and Human Services Secretary Robert F. Kennedy Jr. is at the center of a national debate over vaccine access, safety, and government authority. Just seven months after assuring senators during his January confirmation hearings that he would protect vaccine access, Kennedy’s actions have triggered a cascade of regulatory changes and political rifts that are reverberating from the White House to state capitols and even Wall Street.
Under Kennedy’s tenure, the Centers for Disease Control and Prevention (CDC) has been upended. In June, all 17 members of the CDC’s independent advisory panel on immunization were dismissed and replaced with several known vaccine skeptics. Kennedy justified the reshuffle as a move "to re-establish public confidence in vaccine science." But for many public health experts, the changes have only sown confusion and mistrust, especially as states begin to chart their own courses on vaccine policy, diverging sharply from the Trump administration’s guidelines, according to reporting by The Washington Post.
Perhaps the most controversial move came when Kennedy canceled $500 million in federal funding for mRNA vaccines targeting viruses like influenza and Covid-19. By late August, the CDC’s director, Susan Monarez, was removed just weeks into her role, further fueling uncertainty. Meanwhile, the Food and Drug Administration (FDA) narrowed approval of updated Covid-19 shots for people under 65, restricting eligibility to those with at least one underlying condition. Even those living with high-risk individuals are now excluded from eligibility, a change that has left states scrambling as the virus season approaches.
Some states, particularly those led by Democrats, are mobilizing to preserve vaccine access. On September 10, the governors of Washington, Oregon, California, and Hawaii launched the West Coast Health Alliance, pledging to issue their own vaccine recommendations and counter what California Governor Gavin Newsom called the "destruction" inflicted on the CDC. The alliance aims to provide residents with scientific data on vaccine safety and efficacy and to issue guidance on vaccines for respiratory illnesses and childhood immunizations.
Just hours after the alliance was announced, Florida moved in the opposite direction, becoming the first state to abolish school vaccine mandates. Florida Surgeon General Joseph Ladapo, in a Tampa news conference, denounced mandates as "a violation of bodily autonomy" and declared, "Every last one of them is wrong and drips with disdain and slavery." Governor Ron DeSantis endorsed the plan, though whether it will require legislative input remains unclear. The decision appears at odds with Florida parents, who, according to a recent KFF-Washington Post poll, overwhelmingly support childhood vaccine requirements.
Elsewhere, states are taking a variety of approaches. New Mexico, Massachusetts, Pennsylvania, and Colorado have issued orders allowing pharmacies to administer Covid-19 vaccines without prescriptions. Massachusetts Governor Maura Healey ordered insurers to cover all immunizations recommended by the state Department of Public Health, regardless of federal endorsement. New York Governor Kathy Hochul signed an executive order protecting near-universal access to Covid-19 vaccines through early October, and Minnesota’s Governor Tim Walz followed suit with a similar measure. New Jersey expanded vaccine access to anyone six months or older, and Virginia Health Commissioner Karen Shelton cleared the way for adults 65 and over, as well as certain younger adults with medical conditions, to receive coronavirus vaccines in pharmacies without a prescription. Illinois, meanwhile, remains undecided, with formal guidance expected by the end of September.
"In the absence of federal leadership, we will have 50 states doing 50 different things," said Kyle McGowan, a former chief of staff at the CDC during the first Trump administration, in an interview with The Washington Post. "We saw this during the early stages of Covid-19 as well with states just doing what they hoped was right because of the chaos at the federal level."
The political stakes are high. While President Donald Trump continues to tout Operation Warp Speed—the program that accelerated Covid-19 vaccine development—as one of his greatest achievements, he faces a growing flashpoint over Kennedy’s anti-vaccination agenda. During a recent Senate Finance Committee hearing, Kennedy was pressed on his department’s upheaval and his own views. Republican Senator Bill Cassidy pointedly asked Kennedy whether he agreed the president deserved a Nobel Prize for spearheading Operation Warp Speed. Kennedy replied, "Absolutely, senator." Cassidy noted the contradiction, highlighting Kennedy’s long history of vaccine skepticism—he previously chaired the anti-vaccine group Children’s Health Defense and has promoted debunked claims linking vaccines to autism.
Florida’s move to lift vaccine mandates for schoolchildren drew national attention. State health officials said the changes would likely take effect within 90 days and would eliminate requirements for vaccines against hepatitis B, chickenpox, Hib influenza, and pneumococcal diseases, while maintaining mandates for measles, polio, diphtheria, pertussis, mumps, and tetanus. The plan was endorsed by Kennedy’s administrator for Medicare and Medicaid Services, Dr. Mehmet Oz, who told Fox News, "I would definitely not have mandates for vaccinations."
As Kennedy’s messaging gains traction in some states, others are doubling down on science-based recommendations. The American Academy of Pediatrics continues to recommend annual vaccination for children aged six months to 23 months, and optionally for older children. Vaccine manufacturers, including Moderna and Pfizer, have defended their products’ safety records, emphasizing that more than a billion doses have been administered worldwide without new safety concerns in children or pregnant women. CDC data show death rates after mRNA vaccination remain below those in the general population.
Despite these reassurances, the Trump administration is preparing to present claims linking Covid-19 vaccines to the deaths of 25 children at an upcoming CDC advisory committee meeting. The data comes from the Vaccine Adverse Event Reporting System (VAERS)—a database of unverified reports. FDA Commissioner Marty Makary confirmed on CNN that the agency is reviewing the reports, including autopsy findings and family interviews, but emphasized that the review could take months and that causation has not been established. The Department of Health and Human Services stated that "until official analyses are released, this remains pure speculation."
News of the planned presentation rattled financial markets: Moderna’s stock closed down 7.4%, BioNTech fell 7.3%, Pfizer dropped 4%, and Novavax lost 3.6% on September 12. Critics argue that focusing on unverified reports from VAERS risks downplaying the dangers of Covid-19 itself. Public health professor Noel Brewer told The Washington Post, "They are leveraging this platform to share untruths about vaccines to scare people. The U.S. government is now in the business of vaccine misinformation."
The result is a nation divided—not just along party lines, but within parties themselves. Some Republicans who once supported Kennedy’s appointment are now alarmed by his actions, while Democrats are scrambling to protect vaccine access. Meanwhile, routine childhood vaccination rates are slipping, and the U.S. is experiencing its largest measles outbreak in 25 years.
As states and federal agencies continue to clash, the coming months will test whether Kennedy’s approach will reshape American public health—or whether the backlash will force a course correction. For now, the only certainty is uncertainty, as Americans navigate a patchwork of vaccine policies in a time of deepening mistrust and political polarization.
