Trump Administration Pares Recommended Childhood Vaccinations, Removes Medicaid/CHIP Quality Measures
States have a pivotal role as these additional unilateral actions threaten to weaken vaccine uptake and reshape national immunization norms.
Author: Mandy Cohen, Emily Carrier and Liz Dervan
Editor: Patti Boozang and Amanda Eisenberg
tl;dr
The Department of Health and Human Services (HHS) on Jan. 5 announced a reduction in the number of recommended pediatric vaccines — the most significant change to the nation’s vaccine schedule since President Trump took office and appointed longtime vaccine critic Robert F. Kennedy Jr. as HHS secretary. The new schedule recommends for routine use 11 vaccines, down from 17, and narrows other routine vaccine recommendations to “high-risk” groups. It moves other “non-consensus” vaccines, like the flu shot, to the “shared clinical decision-making” category to “allow for more flexibility and choice, with less coercion,” according to the 25-page assessment released by HHS on Jan. 2.
This change creates significant confusion, further eroding vaccine confidence and creating new challenges for families and clinicians around scope of practice, liability, clinical workflow and vaccine supply issues. This fundamental shift in vaccine policy occurs as rates of timely receipt of MMR and other vaccinations fall and vaccine-preventable diseases continue to increase — most prominently measles, where the US has topped 2,000 cases and is at risk of losing its elimination status.
It also follows CMS removing all childhood vaccination quality measures from the 2026 and 2027 Medicaid Core Sets of Health Care Quality measures, which the federal agency and states use to measure the quality of care delivered to about 78 million Medicaid and Children’s Health Insurance Program (CHIP) beneficiaries — 37 million of whom are children.
Together, these actions destabilize an interconnected system of vaccine access, weaken clinical guidance and undermine public confidence in immunizations. Hope is not lost, however. States can play a pivotal role in ensuring access and maintaining vaccine confidence.
The 80 Million Impact
Following a Dec. 5, 2025, directive from President Trump, HHS has unilaterally updated the nation’s childhood immunization schedule (as shown in the table below) to align with “best practices from peer, developed countries.” The federal agency pointed to Denmark, a country with a population approximately the same size as Miami-Fort Lauderdale that is notable among the United States’ peer countries for its low number of recommended vaccinations, and also for its health system that offers universal access to care and its low rates of disease.
The schedule was amended by HHS without public comment or initial review of the evidence by designated advisory bodies. It organizes the nation’s childhood immunization schedule into three distinct categories:
Recommended immunizations for all children:
Measles, mumps, rubella, polio, pertussis, tetanus, diphtheria, Haemophilus influenzae type B (Hib), pneumococcal disease, human papillomavirus (HPV) and varicella (chickenpox).
Recommended immunizations for high-risk individuals:
Respiratory syncytial virus (RSV), hepatitis A, hepatitis B, dengue, meningococcal ACWY and meningococcal B.
Immunizations based on shared clinical decision-making:
Rotavirus, Covid-19, influenza, meningococcal disease, hepatitis A and hepatitis B.
HHS underscored that all vaccines recommended as of Dec. 31, 2025, will continue to be fully covered by Affordable Care Act insurance plans and federal insurance programs, including Medicaid, CHIP and the Vaccines for Children (VFC) Program. However, continuing a trend from last year’s vaccine policy shifts, these new recommendations will likely create operational challenges for states and clinicians, increase vaccine access challenges for families and further sow confusion and erode public trust in the safety and efficacy of vaccines.
Americans can expect to see barriers and burdens due to this and other administration actions contributing to the shifting vaccination landscape. The change to the vaccine schedule may have implications for who can administer vaccines at the state level. Moving from “routine” to “shared clinical decision-making” may mean that pharmacists, nurses and medical assistants can no longer administer those vaccines, which would have major implications for vaccine access in many communities. To avoid any disruption to access, states can update scope-of-practice laws and issue standing orders to preserve flexibility for vaccine administration and delivery capacity.
The CDC’s recommendations may also play a role in federal and state policies on liability protections for vaccinations that are now classified under clinical shared decision-making. Politico reported that supporters of Kennedy’s move to reorganize the childhood immunization schedule hope it opens the door to stripping liability shields for vaccine manufacturers. Should that be the case, patients who claim injury from a vaccine could circumvent the Vaccine Injury Compensation Program, the government’s no-fault alternative to civil courts, and seek damages from pharmaceutical manufacturers. Still, states like New York say they will maintain the liability protections for vaccines that were previously recommended under the 2025 schedule.
Likewise, the change to the childhood immunization schedule will have ripple effects on manufacturers, who rely on the existing schedule to produce vaccines. As such, the vaccine supply chain may be disrupted — potentially leading to shortages or higher prices for providers, which could further hinder vaccine access for children and families. Schools and day care centers, which follow state vaccination requirements that are informed by CDC recommendations, will also require clarity moving forward. State action may be needed to clarify or amend those requirements for vaccines recommended for shared clinical decision-making.
As detailed in a recent New England Journal of Medicine article, the CDC’s recommendation to vaccinate based on shared clinical decision-making “does not meaningfully change the clinical interaction [between patient and provider] but rather serves to mislead and introduce more paperwork and perceived clinician liability into an already complex system.” In essence, by introducing the concept that these vaccines are “optional,” it implies that they are less safe or important than vaccines recommended for routine use. This may, in turn, heighten vaccine skepticism among the public and generate provider confusion about which vaccines to recommend or how to communicate about them.
CMS Removes Data Tracking Requirements
The downgrading of recommended vaccines follows a last-minute change to CMS’ Medicaid and CHIP Core Sets of Health Care Quality Measures, better known as the “Child and Adult Core Sets.” These sets are standardized measures used to conduct national assessments of quality performance in state Medicaid programs and were made mandatory in 2024. The measure sets are required by law to be “valid, reliable, and evidence-based” and to provide information on “quality of care in relation to the preventive needs of children.”
In a SHO letter titled “2027 Updates to the Child and Adult Core Health Care Quality Measurement Sets and Mandatory Reporting Guidance,” CMS notified states of a significant change signaling how the Trump administration’s position on vaccines could shape the health of half of America’s children who rely on Medicaid and CHIP: All vaccination-related quality measures have now been removed from mandatory quality reporting from state Medicaid programs to CMS.
Under HHS’ new policy, states will have the option to continue collecting and reporting these measures to CMS on a voluntary basis. Notably, states must still collect data on vaccination for other programs, such as the VFC Program, which provides free vaccines for children who are Medicaid-eligible, uninsured or underinsured (with health insurance that does not cover vaccines), as well as to administer vaccination requirements for school attendance, among other functions. In addition, some state governors are joining together to collaborate on public health initiatives, which could include jointly reporting vaccination performance to facilitate the kinds of cross-state comparisons and insights the core sets were intended to offer.
The SHO letter specifically noted that states choosing to report these measures on a voluntary basis are strongly discouraged (but not prohibited) from using them in programs linking financial incentives to performance, such as value-based purchasing programs.
(Core measure sets include a variety of other measures that assess areas where the administration has expressed concern, such as use of contraception and use of pharmacotherapy for psychiatric conditions. These measurement areas could represent additional opportunities for the administration to promote its priorities in ways that profoundly affect the health of Medicaid enrollees.)
The Bottom Line
The federal reorganization of the childhood immunization schedule and the removal of mandatory reporting for long-standing quality metrics come at a precarious time — just as vaccine-preventable diseases like measles and pertussis are reemerging. These actions risk undermining public health by creating confusion and new barriers for families and providers. In this environment, the responsibility to protect children’s health will increasingly fall to the states.
States now have a pivotal opportunity — and obligation — to fill the gap left by federal retrenchment. They can ensure continued access to the full range of childhood immunizations recommended by the American Academy of Pediatrics and the American Academy of Family Physicians, all of which remain covered with no out-of-pocket cost by commercial health coverage, Medicaid, and the VFC Program, as affirmed by HHS. States and providers will be equally critical to continued tracking and reporting vaccine administration data for compliance, outbreak response, and school entry requirements.
To support these efforts, states can leverage resources like the State Health and Value Strategies Vaccine Toolkit, developed by Manatt, which offers practical guidance for maintaining and improving vaccine access, addressing operational challenges, and communicating effectively with the public. This toolkit provides actionable strategies for states to safeguard immunization rates and public health in the face of federal policy shifts.