Doctors' Groups Issue Their Own Flu, COVID and RSV Vaccine Guidance as CDC's Fall Recommendations Stay Stalled

Since Health and Human Services Secretary Robert F. Kennedy Jr. began pulling back longstanding federal vaccine recommendations last year, the Centers for Disease Control and Prevention has not issued updated guidance for how Americans should use this fall's flu, COVID-19 and RSV vaccines. On Wednesday, four of the country's largest medical organizations stepped into that gap.

The American Academy of Pediatrics, the American Academy of Family Physicians, the American College of Obstetricians and Gynecologists, and the Infectious Diseases Society of America simultaneously published vaccination guidelines for the 2026-27 season, according to Fierce Healthcare. The groups say they're filling a vacuum the federal government has left open.

"There's been a lot of confusion and chaos regarding vaccine recommendations," said Dr. Sandra Fryhofer of the American Medical Association, according to the Associated Press. She said the goal is giving the public "clear, consistent, science-based guidance even while the federal process is in flux."

What the science review found

The guidance leans on an independent evidence review from the Vaccine Integrity Project, an initiative based at the University of Minnesota, done in collaboration with the AMA. Researchers examined hundreds of peer-reviewed studies published since August 2025 on flu, COVID and RSV vaccines. The findings were published Wednesday in JAMA.

The review found the vaccines continue to provide meaningful protection against severe illness, hospitalization and death, and identified no new safety concerns, according to Fierce Healthcare. Flu vaccination specifically was tied to a 31% reduction in hospitalizations among older adults, per the review.

"Immunization continues to be one of our best tools for preventing severe illness from respiratory viruses," said Dr. Michael Osterholm, the Vaccine Integrity Project's executive director. "This year's review confirms that the newest evidence remains consistent with research showing these immunizations reduce the risk of hospitalization and death among the people most likely to experience serious disease."

This year also brings a new option: a flu shot for people 50 and older built on the same mRNA platform used in COVID vaccines. One study found Moderna's mFlusiva was 27% more effective than the comparison vaccine used in that trial, according to the AP, though the AAFP's Dr. Sarah Nosal said seniors shouldn't delay vaccination if that specific shot isn't available.

Where the doctors' groups and federal guidance diverge

The new guidelines go further than current federal advice on some points. The medical groups recommend routine COVID vaccination for healthy younger adults, young children and pregnant women, according to NPR, groups the current federal guidance does not routinely recommend.

"We cannot allow the breakdown of the federal process to create a vacuum in evidence-based vaccine guidance," said Dr. Bruce Gellin of the Vaccine Integrity Project, according to NPR.

The CDC did not respond to questions from the AP about any updated fall guidance, but suggested on its website that doctors follow last year's flu recommendations. The CDC's Advisory Committee on Immunization Practices, which normally shapes state and insurance vaccine policy, remains tied up in litigation over the administration's attempt to reduce the number of vaccines recommended for children.

The MMR-splitting fight, separately

A related but distinct fight is playing out over childhood vaccines specifically. President Trump has signed an executive order calling for splitting the combined measles-mumps-rubella shot into three separate vaccinations, according to the Epoch Times.

A White House spokesman told the Epoch Times the change "will give parents more options on timing and frequency," arguing it could ultimately raise vaccination rates for all three diseases. Dr. Michael Segal, a neurologist, told the Epoch Times that giving three vaccines simultaneously produces more peak inflammation than staggering them, and pointed to 2007 research linking seizure disorders after vaccination to variants in the SCN1A gene. "If my kids were now at the age of getting vaccinations, I would definitely prefer the three separate vaccinations," Segal said.

The sources here don't show the major pediatric groups endorsing the split, and Merck, which stopped selling separate MMR components in the 2000s, has told the Epoch Times that reformulating standalone vaccines could take up to 10 years. Merck's 2009 rationale for combining the shots was reducing vaccination delays, not addressing an inflammation risk.

Vaccination rates broadly, including for measles, have declined since 2020, according to the Epoch Times, a trend Dr. Monique Yohanan of the Independent Women's Forum attributed to pandemic-era school closures and eroded public trust rather than any single policy change.

What happens next depends largely on the courts. The lawsuit blocking the administration's changes to the childhood vaccine schedule remains unresolved, and no timeline for a ruling has been reported. Until it clears, families and insurers are left choosing between CDC's frozen guidance and the newer recommendations from AAP, AAFP, ACOG and IDSA, four organizations with no regulatory authority but the only ones offering an updated answer.