CDC Vaccine Guidance Stalls Amid ACIP Overhaul Under Kennedy

The Centers for Disease Control and Prevention has made no recommendation on a newly approved flu vaccine and has stalled other immunization guidance, months after Health Secretary Robert F. Kennedy Jr. dismissed the Advisory Committee on Immunization Practices and replaced it with a panel that includes anti-vaccine voices, according to reporting published between September 25 and 27, 2026.¹²⁵

A vaccine without a recommendation

The FDA recently approved mFlusiva, described as the first flu vaccine built on mRNA technology, granting full approval for people ages 50 to 64 after the shot performed well in older adults in testing. The CDC, however, has made no recommendation on the vaccine. It posted that it would maintain last year's flu vaccine endorsements instead, citing legal uncertainties, and mFlusiva does not appear among the flu vaccines currently listed as recommended to the public this fall.¹²³⁴

According to Fast Company and the Associated Press, the inaction marks a break from the CDC's longstanding practice. Medical societies are nonetheless recommending mFlusiva as an option for patients.¹³

ACIP dismantled

The Advisory Committee on Immunization Practices had guided CDC vaccine recommendations for 60 years before Kennedy dismissed it and replaced it with a group that includes anti-vaccine voices. As a result, the agency's system for evaluating and endorsing vaccines has been thrown into disarray, with officials making little forward progress, the AP and ksat.com reported. Fast Company and the AP also reported that vaccine-wary officials within the Trump administration have attempted to scale back vaccine recommendations more broadly.¹²³⁴

Yale researcher Jason Schwartz, who studies government health agencies, said the breakdown leaves no clear path for updating guidance even when evidence shifts. "We find ourselves at a point where even if credible evidence has reached a tipping point, we don't have an obvious mechanism that can formalize that change," he said.²

HPV dose cut suspended by court

ACIP had formed a working group in 2024 to reassess HPV vaccine recommendations. In January, Kennedy decided to reduce recommended HPV vaccine doses from two to one as part of a broader contraction of the childhood vaccination schedule, even as recent research suggested one shot could be sufficient, at least for girls. Separately, the American Academy of Pediatrics is reconsidering its own guidance on the HPV shot and may settle on a decision before the year is out.¹²⁴⁵

In March, a federal judge suspended Kennedy's HPV dose-reduction decision, ruled that he had likely violated federal procedures, and stopped his newly installed panel from holding further meetings. The American Academy of Pediatrics and other medical groups sued Kennedy over the vaccine policy changes. American College of Physicians president Jason Goldman welcomed the ruling, saying it would mean "a return to a transparent and evidence-driven process that safeguards the health of all communities and the best interests of our patients."¹³⁴⁵

RSV, COVID and pending category changes

ACIP had previously recommended that the RSV vaccine be given between September and January across most of the country. Medical groups have since said the shot should be offered through the beginning of March instead. In a related development, updated COVID-19 shots received FDA approval, though for much of the summer officials stayed silent on whether the Vaccines for Children program would include them; they have since clarified that the program will now accept orders for the new doses.¹²³⁴

The Trump administration is also considering changes to the federal government's vaccine recommendation categories, though no specific proposal has been released; public comments on the potential changes were due this week. The Governors Public Health Alliance, a coalition of 15 governors from Democratic states, warned that the anticipated changes would probably muddy the picture further. Its managing director, Angela Botticella, said, "It's Governors and their residents who bear the brunt of any increased disease outbreaks due to confusion related to hastily made federal changes." Chris Regal of America's Health Insurance Plans said of the shifting landscape, "We all recognized this needs to evolve." Schwartz added that the administration's credibility on vaccines has been damaged. "The credibility of the Trump administration, when it comes to vaccine recommendations, is so compromised in the eyes of the mainstream medical and public health communities that even recommendations that might align with where the public health community was trending are likely to be viewed with skepticism or distrust," he said.²