Food and Drug Administration Commissioner Marty Makary signed off on the ouster of top vaccine official Peter Marks shortly after being quietly sworn in as the agency’s new leader late last week, four people familiar with the matter told POLITICO.
The forced removal was Makary’s first major act as commissioner and sent a powerful signal to a stunned Washington that was already anxious about the role vaccine skepticism would play under Secretary Robert F. Kennedy Jr.’s Health and Human Services Department. Makary and Kennedy had previously agreed to push out Marks, who led the FDA’s vaccine division for more than eight years, as part of a broader overhaul of HHS leadership.
The decision has alarmed lawmakers and the pharmaceutical industry, who see it as an effort by Kennedy to lay the groundwork for remaking the government’s approach to vaccines after years of sowing doubts about the shots.
While Kennedy made the final call to force Marks’ exit, he did so only after Makary consented, said the people familiar, who were granted anonymity to discuss private deliberations. Makary was sworn in late last week, according to multiple people granted anonymity to discuss the timing.
Makary’s involvement in the decision was not widely known even within the FDA, which has yet to acknowledge that he’s already been sworn in as head of the agency. On the agency's website, Sara Brenner is still listed as the acting commissioner of food and drugs.
Even Marks appeared unaware of Makary’s status on Friday, addressing his resignation letter to Brenner and using his parting words to take aim at Kennedy. Marks declined to comment.
"I was willing to work to address the Secretary's concerns regarding vaccine safety and transparency," Marks wrote. "However, it has become clear that truth and transparency are not desired by the Secretary, but rather he wishes subservient confirmation of his misinformation and lies."
Makary’s support for driving out Marks is likely to further unsettle drug companies and supporters of the FDA, who had hoped that the former Johns Hopkins surgeon and researcher would serve as a bulwark against major changes to the nation’s vaccine policies.
Makary gained prominence in recent years as a vocal critic of the FDA and of the government’s response to the Covid pandemic. But unlike Kennedy, he has generally supported vaccines and never embraced the debunked theory advanced by the HHS secretary that they are linked to autism.
The Senate confirmed Makary to run the FDA last Tuesday. But he was not expected to begin working out of his office at the agency until this week, the people said.
An HHS spokesperson declined to comment. The Pink Sheet first reported the timing of Makary's swearing in.
Makary has discussed seeking additional changes across the FDA in his first weeks, including installing new leadership at another major center within the agency, the Center for Tobacco Products, three of the people said.
That potential change would come on top of the upheaval already underway at the FDA. Since Trump’s election, the agency’s top drug and food officials have quit, as well as its principal deputy commissioner. A sweeping reorganization that Kennedy announced last week would reduce the agency’s staff by 3,500 over the next several weeks.
But amid the restructuring, Marks’ ouster has generated outsize concern within the FDA and across the health care landscape. Vaccine manufacturers Moderna and Novavax saw their stocks drop sharply when the market opened Monday.
Biotechnology Innovation Organization President and CEO John Crowley said the loss of leadership at the FDA could erode scientific standards and impact the development of new medicines.
“We advocated strongly for Peter’s continued leadership,” Crowley texted.
While at times a polarizing figure at the agency, Marks is credited with helping establish the Operation Warp Speed initiative during President Donald Trump’s first term that delivered a Covid vaccine in a matter of months.
The vaccine regulator had won the trust of FDA commissioners and lawmakers in both parties, developing a reputation over more than 12 years at the FDA's Center for Biologics Evaluation and Research as a fierce defender of scientific independence and the agency's rigorous approach to developing and testing vaccines.
“Peter’s commitment to bringing the best science and data to the development and availability of lifesaving biomedical technologies, from gene and cell therapies to the Trump Administration’s Operation Warp Speed, has saved countless lives,” Mark McClellan, who ran the FDA during the George W. Bush administration, told POLITICO. “His decade-long leadership at the FDA is a big reason why the FDA is the gold standard for advancing the most innovative breakthrough medicines."
Robert Califf, commissioner during the Biden administration, said last week that Marks’ “interest was always with the combination of public health and the special needs of patients.”
"The role of the FDA Commissioner is largely to fend off political interference so that career civil servants without financial conflicts can make decisions based upon the statutes and rules governing these decisions," Califf wrote in a LinkedIn post on Monday.
Sen. Bill Cassidy (R-La.), a physician who cast a crucial vote in favor of Kennedy’s confirmation, said in a statement Saturday that Makary and Kennedy should “replace him with someone of similar stature and credibility amongst the scientific community,” adding that Marks’ departure was “a loss to the FDA.”
But Kennedy and his allies — which include prominent anti-vaccine figures — had long expressed skepticism of Marks and the FDA’s approach to vaccines, often accusing the agency without evidence of downplaying the health risks they believe the shots pose.
The HHS secretary said during a NewsNation interview last week that he wants to create an office within the Centers for Disease Control and Prevention that would specialize in “vaccine injuries.” Kennedy also ordered a large-scale study on potential links between vaccines and autism, despite extensive research that has failed to find evidence of such a connection.
Kennedy’s approach to the measles outbreak put him at odds with Marks as well, the vaccine regulator wrote in his resignation letter. Kennedy has offered only tepid support for the measles vaccine while also promoting the questionable use of vitamin A supplements as a treatment for the disease.
"Undermining confidence in well-established vaccines that have met high standards for quality, safety, and effectiveness that have been in place for decades at FDA is irresponsible, detrimental to public health, and a clear danger to our nation's health, safety, and security," Marks wrote.
In a statement shortly after Marks' resignation, an HHS official blamed Marks for failing to support Kennedy's goals and said "he has no place at FDA under the strong leadership of Secretary Kennedy."
Makary has yet publicly addressed Marks' departure.
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