Kids are heading back to school this fall as the country experiences some of the lowest childhood vaccine rates and highest levels of public health uncertainty in known memory.
Amid the swirling currents: the defunding of vaccine research and competing messaging around COVID shots for children; a rare federal attempt to influence a West Virginia legal battle over childhood vaccine exemptions; and a dramatic leadership struggle within the Centers for Disease Control and Prevention that could solidify more power in the hands of Health and Human Services Secretary Robert F. Kennedy Jr.
Kennedy is seen by many as the destabilizing figure at the center of the chaos, and 2025-26 will be the first full school year that the longtime vaccine skeptic is in charge of childhood public health. The controversial secretary, who earned a public rebuke this week from every one of his predecessors going back to the Carter administration, is scheduled to testify before the Senate Finance Committee later today.
Sen. Bill Cassidy, R-Louisiana, who heads the Senate health committee and played a pivotal role in Kennedy’s confirmation, has called for committee oversight of the CDC amid the turmoil, citing children’s health as his major concern.
The governors of California, Oregon and Washington said the alliance will “ensure residents remain protected by science, not politics.” Meanwhile, Florida Gov. Ron DeSantis and his surgeon general announced their intention Wednesday to become the first state to drop all vaccine mandates, including for schoolchildren.
As the states splintered on vaccines, 1,000 current and former HHS staff released an open letter formally calling for Kennedy’s resignation, writing that he “continues to endanger the nation’s health.” The group condemned a series of actions including the recent firing of the Senate-confirmed CDC director, Kennedy’s refusal to be briefed by CDC experts on vaccine-preventable diseases and his “misleading claims” about physician and hospital liability for following vaccine guidance that he opposes.
They also denounced the Food and Drug Administration’s recent revocation of emergency use authorization for COVID vaccines, which — alongside the the CDC’s newest recommendations — will likely make it significantly harder for children, especially those under 5 years old, to access the shots. Recently released FDA memos show its vaccine chief overruled staff scientists who, citing high hospitalization rates among young children with COVID, recommended a wide range of age groups continue to get the vaccine, according to The New York Times.
All of this, partnered with Kennedy’s long history of disseminating scientific misinformation, including the debunked claim that vaccines can cause autism, has led to great confusion for parents just as their kids are returning to school. Kennedy has promised to release a study later this month, which he said would expose “what the environmental toxins are that are causing” autism.
“There is a lot of inaccurate information right now coming from the highest levels of HHS,” said Kawsar Talaat, physician and associate professor at the Johns Hopkins Bloomberg School of Public Health, whose research focuses on vaccines. “I would think that for family members, who don’t necessarily have expertise, it would be hard to know who to trust, and it will certainly contribute to a decline in vaccination rates.”
Indeed, during the 2024-25 school year, immunization rates among kindergarteners across the country decreased for all reported vaccines, according to the latest available CDC data. Rates for the measles, mumps, and rubella vaccine fell to 92.5% from approximately 95% pre-pandemic. And over three-quarters of states had MMR vaccination rates below the 95% needed for herd immunity, with some, like Idaho at 78.5%, well below it.
As these numbers were falling, exemptions to mandatory vaccines for school-aged kids were on the rise, increasing to 3.6% nationally, driven by non-medical exemptions and up from 2.5% in the 2019-20 school year. Seventeen states — spiking from nine states pre-pandemic — reported exemptions exceeding 5%, threatening herd immunity.
Lynn Nelson is the president of The National Association of School Nurses and has seen this uncertainty and hesitancy firsthand.
“We get a lot of families who are confused,” she said, “who may have immunized children until this point and now are having second thoughts about it.”
Increasingly, conflicted parents are bringing messages they’ve heard from HHS or Kennedy himself to their school nurses, wondering why they contradict what they’ve historically been told by their pediatricians.
“It tends to be things like, “Well, it sounds like maybe autism is caused by [vaccines]. We want to wait and see,’” Nelson said.
But as these parents hold off on immunizing their kids, communities remain at heightened risk for infection and outbreak, she added.
And even if medical providers are able to fight the misinformation and have conversations with parents that ultimately lead them to want to vaccinate, some kids might not be able to access the shots, amid funding cuts to public health vaccination clinics in rural areas.
Vaccine hesitancy also plays out at the district level, since school system leaders are “just as susceptible to misinformation as anyone else” and they often make the decision on whether or not to enforce the policies requiring most children be vaccinated in order to attend school, Nelson said.
“It’s a question for most of us probably of when — not if — there’s going to be an outbreak.”
Chaos and pushback at the CDC
An already anxious back-to-school season for mandatory immunizations was intensified by the firing of CDC head Susan Monarez on Aug. 27, and her subsequent refusal to leave the post, following a clash over vaccine policy, according to reporting by The New York Times.
Monarez’s lawyers claimed her removal was “legally deficient,” and said, “the attack on Dr. Monarez is a warning to every American: Our evidence-based systems are being undermined from within.”
She has since been replaced by Jim O’Neill, who has no medical training and, during the pandemic, posted conspiracy theories on social media and voiced support for unproven treatments — such as ivermectin, according to reporting by The Guardian. Before being appointed as acting head of the CDC, O’Neill served as a HHS deputy to Kennedy.
At least four other powerful agency leaders resigned, some with scathing letters on X, claiming they were asked to participate in an unscientific vaccine recommendation process.
My resignation letter from CDC.
Dear Dr. Houry,
I am writing to formally resign from my position as Director of the National Center for Immunization and Respiratory Diseases at the Centers for Disease Control and Prevention (CDC), effective August 28, 2025, close of business.…
— DrDemetre (@dr_demetre) August 27, 2025
In response, CDC employees staged a mass walkout — a “clap out” protest to show support for their departing colleagues. An August investigation by ProPublica revealed how badly the department has been depleted under Kennedy, with at least 20,500 total HHS workers gone since January, including at least 15% of all CDC staff.
Last week’s high-profile exodus comes after a tumultuous month: On Aug. 20, over 750 employees of the CDC and other health agencies signed a rare open letter, imploring Kennedy to stop spreading misinformation. The authors argued his rhetoric contributed to an attack earlier that month on their headquarters by a gunman who fired more than 500 rounds onto the agency’s main campus and appeared to be, at least in part, motivated by COVID vaccine misinformation.
“Health and Human Services Secretary Robert F. Kennedy, Jr., is complicit in dismantling America’s public health infrastructure and endangering the nation’s health by repeatedly spreading inaccurate health information,” the letter reads. The authors accused Kennedy of sowing public mistrust in the CDC’s workforce; firing critical workers; making false and dangerous claims about mRNA and measles vaccines; and misusing data to falsely claim childhood vaccines are the cause of autism.
HHS did not respond to requests for comment on the confusion surrounding vaccine policies nor on the allegations that inaccurate information is coming out of the agency, eroding faith in its work.
In response to mounting criticism, Kennedy published an op-ed in The Wall Street Journal this week, arguing he was, “restoring public trust in the CDC,” which had been destroyed by “bureaucratic inertia, politicized science and mission creep.”
“We have shown what a focused CDC can achieve,” he wrote, citing and defending his response to the measles outbreak, which he said, “was neither ‘pro-vax’ nor ‘antivax.’”
He identified six areas of focus, including investing in the workforce, that he wrote will “restore the CDC’s focus on infectious disease, invest in innovation, and rebuild trust through integrity and transparency.”
The American Association of Pediatrics recently signaled its lack of confidence by filing a lawsuit, alongside a number of other health care organizations, arguing Kennedy had violated federal law and made “unilateral, unscientific changes to federal vaccine policy” by moving to curb COVID vaccines for young children. The plaintiffs include an immunocompromised mother to two teenage boys who were denied COVID vaccines.
They’ve also issued their own guidance, continuing to recommend the COVID vaccines for all young children. Kennedy responded to this move on X, calling it a “list of corporate-friendly vaccine recommendations” and “perhaps, just a pay-to-play scheme.”
Last week, the Food and Drug Administration approved updated COVID vaccines, but with new restrictions: they’ll only be available to people 65 and older or younger people with at least one underlying medical condition that increases their risk for severe disease. In a post on X, Kennedy said the Moderna vaccine had been approved for use in those older than 6 months, Pfizer in those older than 5 years and Novavax in those older than 12 years.
“These vaccines are available for all patients who choose them after consulting with their doctors,” he wrote, though it’s still not clear who will have the shots covered by insurance.
While healthy children and adults without underlying conditions were eligible to receive the vaccine historically, HHS claimed, “Today’s decision does not affect access to these vaccines for healthy individuals.”
“HHS is not limiting access,” a department spokesperson wrote to The 74. “The COVID vaccine remains available for anyone who chooses it in consultation with their healthcare provider.”
In response to a request for clarification to determine if this means children and healthy adults under 65 can access the vaccine with permission from a doctor, the agency spokesperson just repeated the same language.
All of this back and forth has contributed to confusion for parents, as COVID levels increase in many areas of the country. Recent polling by KFF, a nonpartisan, nonprofit health policy organization, found that half (48%) of parents are not sure if federal health agencies are currently recommending that healthy children receive a COVID vaccine this fall or not.
A federal push for vaccine exemptions
While many eyes are on the debate surrounding COVID vaccines, researchers and physicians also remain laser focused on measles, following this year’s outbreak, which infected over 1,300 people across 41 states and killed two unvaccinated children.
Case numbers this year are already the highest they’ve been since the disease was declared eradicated in the U.S. in 2000. Some 92% of reported infections have involved a person who was unvaccinated or whose status was unknown and 13% have resulted in hospitalization.
Throughout the outbreaks, Kennedy has downplayed the severity and has been inconsistent in his support of the MMR vaccine.
In a recent and highly unusual move for the federal government, Kennedy expressed his support for a philosophical and religious exemption to mandatory vaccines for school-aged kids in West Virginia.
Up until a recent executive order opened the door for broader exemptions, the state had some of the nation’s strictest childhood vaccination policies and was one of only five that exclusively allowed for medical exemptions. Already around 500 requests for religious and philosophical exemptions have been submitted — and approved — for the 2025-26 school year, according to records obtained by The 74, though those numbers are not yet reflected in the CDC’s data.
According to that data, Georgia and Michigan saw exemptions rise faster than any other state — by 1.2 percentage points year-over-year — driven almost exclusively by non-medical exemptions. They were closely followed by Idaho, Pennsylvania, South Dakota and Utah.
In West Virginia, conflict between the governor’s order and current state law has led to confusion and legal action over how officials should proceed. Beginning on Aug. 21, the federal government publicly weighed in, apparently attempting to tip the scales.
First, HHS’s Office for Civil Rights sent a letter to all West Virginia health departments participating in the federal Vaccines for Children Program, which provides vaccines to millions of kids who otherwise wouldn’t be able to afford them. The communication stated that if they did not comply with the governor’s executive order, they would no longer be eligible to participate in the program.
Richard Hughes, a George Washington University law professor and leading vaccine law expert, called this move an unheard-of “implied threat.”
“I just think that’s got to be unprecedented for a federal agency — the Office for Civil Rights — to go and pick out a state law and say, ‘You need to comply with that.’ That just boggles my mind,” Hughes said.
“What I worry about is that we’re about to see a push at the federal and the state level encouraging religious exemptions,” he added.
Kennedy followed up with a post on X, voicing his support for the West Virginia governor and urging state legislators to comply.
Del Bigtree, CEO of the Informed Consent Action Network, an anti-vaccine advocacy group, told The 74, “We’re happy that Robert Kennedy Jr. and HHS are supporting Gov. Morrissey. I think this is a pivotal moment for this conversation in this nation.”
Other states have joined West Virginia in pursuit of such bills, according to Caitlin Gilmet, the communications director for American Families for Vaccines, a pro-vaccine advocacy organization formerly called SAFE Communities Coalition.
“We’re seeing medical freedom bills in a number of states. Idaho, Montana, Tennessee, Texas, Florida are all kind of national bellwethers where those parental rights bills are being tested,” she said.
Kids in those states are particularly vulnerable to “new exemption policies, weak enforcement and then the conditions to create exemption clusters,” she added, which can then lead to outbreaks.
A number of these types of bills contain language or policies that are unclear, leading to more confusion and conflicting guidance.
Further complicating the issue is Kennedy’s recent firing of all members of the group responsible for making recommendations on the safety, efficacy and clinical need for vaccines to the CDC as well as the cancellation of $500 million in federal grants to mRNA vaccines, the technology used to develop the COVID vaccination.
In a post on X, he claimed the vaccines are ineffective and cause “more risks than benefits,” while “paradoxically… prolong[ing] pandemics as the virus constantly mutates to escape the protective effects of the vaccines” — assertions that are echoed by activists like Bigtree, yet have been widely debunked by researchers and medical professionals.
“It is incredibly misleading, not to mention just false, to say that the vaccines are more harmful than they are beneficial,” said Talaat, the Johns Hopkins professor. “They are incredibly beneficial. They’ve saved millions of lives.”
While COVID vaccines were the first on the market to use mRNA technology, others were in development before the funding cancellation, including ones to fight cancer and bird flu.
“[Bird flu] could be the next pandemic,” Talaat said, “and they canceled the contracts to create mRNA vaccines against this virus.”
“It’s really important,” she added, “that people understand that, unfortunately, this is not a time where we can trust those in the highest positions of power at HHS.”