Our Vaccine System Is Delicate. Trump Just Threw a Bowling Ball at It.
Parents and pediatricians in the United States are in uncharted territory. As front pages catalog a dizzying array of domestic and international chaos, the U.S. measles outbreak quietly continues to spread at alarming speed; in 2025, we finished the deadliest flu season for children on record outside of a pandemic, only to stumble into a new record-breaking season this year; Covid and RSV continue to surge; diseases that were largely vanquished before many of us were born now threaten a comeback.
Earlier this month, the U.S. announced, under the purview of longtime anti-vaccine activist Robert F. Kennedy Jr., that some vaccines would only be available to high-risk infants, while others would be available under “shared clinical decision-making”—previously a little-known term that meant a vaccine’s benefits were unclear and could only be given on doctors’ orders. The changes reduce the vaccination schedule of the U.S., once a global leader, by a full third. Never before has the United States made such drastic changes to its vaccination schedule or any of its public health guidance so rapidly, and all without input from outside experts or the public.
The new recommendations will likely make it harder for children to get vaccinated—either because providers follow the new guidelines and don’t offer the vaccine to some patients, or because insurance companies and federal programs stop covering the vaccine if it is offered. Confusion may also play a major role. It’s not always clear who is “high risk” and what “shared clinical decision-making” even means, in legal and practical terms. After all, vaccination, and all health decisions, are always shared decisions—with careful explanations of the benefits and the side effects. (No one is bursting into the exam room with a needle and arm restraints, despite anti-vaxxers’ paranoid fantasies.) Parents and providers are still wading through bewildering announcements to understand what, exactly, has changed, and then we’re bombarded with a firehose of misinformation on social media (and, increasingly, in traditional media).
But these changes to the recommended vaccine schedule will also cause another problem: They won’t only take away certain vaccines from kids who no longer qualify. All vaccines may now face supply and demand issues.
“We’ve never had a change for this many vaccines all at once,” Eric Hall, assistant professor of epidemiology at Oregon Health and Science University, told me. Everyone is trying to understand what happens next, and “honestly, we don’t really know.” But, he said, this is the likely scenario: The abrupt change in recommendations will introduce confusion and misunderstanding among parents and providers. More parents will see vaccines as optional, and some will opt out. As fewer children get some or any vaccines, providers start stocking fewer doses and manufacturers may make fewer vaccines.
That means, even if you are eligible under the new restrictions, and you know to ask for the vaccines, and your provider is willing to give the shots, you may still struggle to get them. And the overall slide in confidence could affect vaccines that are still recommended. Your hospital might plan for fewer hepatitis B or RSV shots at birth and run out of stock before your baby is born; your pediatrician might think your baby got those shots at the hospital and decide not to stock so many in their practice. Vaccines are expensive to buy and store; the cost of wasted doses could mean pediatricians—already one of the most underpaid medical professions—can’t afford to keep enough vaccines in stock.
“I do think that can have implications on availability and the supply chain and some of these other pieces that make sure vaccination is available for everybody in the community who wants it,” Hall said.
“These recommendations will create additional confusion, concerns, and challenges,” said Jason Schwartz, associate professor of health policy and management at the Yale School of Public Health—and by creating new doubts about the safety and effectiveness of vaccines, the new limitations “will suppress demand for those vaccines.”
The first bottleneck in the vaccine supply could come with how doses are ordered and reimbursed. For most states, there are two ways that providers usually order vaccines. One is through the federally funded Vaccines for Children (VFC) program, where providers order the shots at no cost and are closely audited on how many they give out. VFC covers more than half of children in the United States: kids who are on Medicaid, uninsured and under-insured, or Alaska Native and American Indian. For the time being, the Trump administration has said it will continue to provide vaccines through VFC, even though some of the shots are now restricted. “My concern,” Hall said, “is we don’t know how long that’s necessarily going to last, or if that will be something that changes down the road as well.”
The other way providers order vaccines is privately through the manufacturer or a distributor, where they must front all costs of the order. This is how the kids who are fully insured via private insurance tend to get their shots. And in theory, even if insurance companies stop covering some of the shots for some kids due to the new guidance, families with funds could get around the problem by paying out of pocket.
But because providers pay up front for vaccines from the private market and monitor VFC doses closely, they only place orders for how many vaccines they expect to give. Even before the recent changes to vaccine guidance, providers already faced challenges in anticipating demand and fronting the expenses associated with vaccines—not just the costs of the shots but also the refrigerators and freezers to hold them and the staff to administer them and file for reimbursement. (While pharmacies are sometimes able to vaccinate children, there are state-level age restrictions on pharmacy vaccine administration and the vast majority of children get vaccinated by their pediatrician or family doctor.)
Providers are “essentially fronting large sums of money to make sure they have the vaccines available,” Schwartz said. “That comes with significant financial exposure.” Some doctors, especially smaller practices, might order less so they don’t go broke if the vaccines aren’t used. And while anti-vaxxers have accused pediatricians of getting rich because of vaccine reimbursements, those payments are “very modest in the grand scheme of medical billing,” because the payments cover the costs of staffing, record-keeping, supplies, and cold storage, Schwartz pointed out.
The new restrictions will make it harder for providers to know how many combination vaccines and how many single-antigen shots they should order. Hepatitis B shots, for instance, are now restricted as both high risk and shared clinical decision-making—which is confusing enough. But the vaccine is often given in combination with HiB (Haemophilus influenzae type b), diphtheria-tetanus-pertussis (DTAP), and polio. If parents want only the fully recommended shots, providers would need to stock three separate vaccines—which incur additional shipping and storage expenses. In addition, some vaccines only come in bulk, and vials meant for multiple doses need to be discarded after a certain amount of time. Vaccines also have a shelf life, so those different expiration dates need to be monitored and juggled.
If a vaccine is delayed—if the hospital doesn’t have it in stock, if a pediatrician’s order is delayed, if parents have worries that aren’t assuaged yet—children are much less likely to get it at all, according to new research. “Anything that introduces friction like that is going to lead to those opportunities being missed,” which is why maintaining a steady supply of vaccines and “avoiding that missed opportunity at all costs is important,” Schwartz said. “Anything that destabilizes the very well-developed, planned, structured cadence of our vaccination program will put providers on their heels, not just in terms of how they help communicate vaccines, but making sure that they continue to maintain the robust vaccine supplies that could be predictable in the past.”
The vast majority of parents support vaccines and do not want their kids to get sick. But the new recommendations, and the misinformation they encounter from top U.S. health officials down through the information ecosystem of the internet, will lead to confusion. Similarly, nearly all providers understand the value of vaccines and want their patients to be protected, but they have limited time at medical visits to cut through all of the noise around vaccines—in addition to all of the other conversations that happen around growth and well-being and developmental milestones. “The more time that goes toward trying to address hypothetical concerns around vaccines that are unfounded, there’ll be less time to address all the other important issues that ought to be included in the well-child visits,” Schwartz said. As The Washington Post recently reported, providers may also need to deal with parents trying to get their kids vaccinated ahead of schedule, because of the new worries about availability.
Some groups are trying to fill the gap left by federal guidance. The new Vaccine Integrity Project at the University of Minnesota conducts exhaustive reviews of the scientific evidence, with which existing and highly respected medical organizations, like the American Academy of Pediatrics, may make recommendations. Researchers at the Yale School of Public Health, for instance, are developing a dashboard to survey outbreaks anywhere in the US. Some states are forming regional alliances, like the West Coast Health Alliance and the Northeast Public Health Collaborative, to preserve access to and recommendations for vaccines and more. Former top officials who were pushed out of U.S. health agencies are now landing at state and local health departments.
But increasingly where you live may determine which vaccines you can get—and your overall risk based on others’ vaccination rates. Vaccine policies are set by states, and until now, states have relied on clear, evidence-based recommendations from the federal government, Hall said. “Now, what we’re seeing is essentially a lot of fragmentation happening.” The fragmentation and polarization are likely to worsen as red states feel financial and political pressure from the Trump administration to step in line. School vaccine mandates, which are set by state and local governments, are facing their greatest threat in generations, Schwartz said. “Your child’s risk of vaccine-preventable disease, on the one hand, will look different based on where you live, and in large part, on the political party in power,” he said. But those geographical differences can only go so far, he added: “As the old saying goes, infectious diseases don’t respect borders.”