FDA's Top Vaccine Official Resigns After RFK Jr. Gave Him 'Ultimatum'

“If Peter Marks does not want to get behind restoring science to its golden standard and promoting radical transparency, then he has no place at FDA..."

The FDA’s top vaccine authority has resigned after RFK Jr. gave him an ultimatum: Step down or be fired.

The move, first reported by The Wall Street Journal, marks a high-profile shakeup at the Department of Health and Human Services (HHS) under Secretary Robert F. Kennedy Jr., who is leading a sweeping restructuring of the agency.

In his resignation letter, Marks accused Secretary Kennedy of rejecting “truth and transparency” in favor of “misinformation and lies.”

The letter, obtained by CNN, followed internal pressure from HHS leadership.

An HHS official responded bluntly: “If Peter Marks does not want to get behind restoring science to its golden standard and promoting radical transparency, then he has no place at FDA under the strong leadership of Secretary Kennedy.”

Marks oversaw the FDA’s Center for Biologics Evaluation and Research, the agency responsible for approving and monitoring vaccines, gene therapies, and blood products. He played a key role in the federal government’s Operation Warp Speed and subsequent vaccine rollouts, which critics say were rushed, politicized, and marred by lack of long-term safety data.

The resignation comes as HHS undergoes a dramatic downsizing. The department announced this week it would eliminate 10,000 positions, shut down the Office of Long COVID, and cancel more than 250 federal grants. Many of the canceled grants were tied to vaccine messaging, DEI initiatives, and other ideologically driven health projects.

“The COVID-19 pandemic is over, and HHS will no longer waste billions of taxpayer dollars responding to a non-existent pandemic that Americans moved on from years ago,” said Andrew Nixon, Director of Communications at HHS.

Columbia University alone lost more than $400 million in federal funding as part of a broader audit of DEI-related spending and campus anti-Semitism. The agency is also consolidating its 28 divisions into 15 and closing half its regional offices.

Critics of the shakeup argue it threatens public health infrastructure. Dr. Ashish Jha, former Biden White House Covid coordinator, called Marks a “brilliant scientist” and said his removal makes the FDA “dramatically weaker.”

Supporters of the reforms say this is long-overdue accountability for a public health apparatus that overstepped during Covid — mandating vaccines, enforcing lockdowns, and undermining dissent while dismissing legitimate scientific debate.

The same officials who told Americans to “follow the science” are now resisting scrutiny of that science.

Among the most controversial changes: HHS has asked the CDC to revisit the question of whether vaccines could be linked to autism — a topic public health agencies had long declared off-limits. Vaccine industry defenders, like Dr. Paul Offit, have warned this could lead to “fear” and more vaccine skepticism.

But for many Americans, it’s not fear — it’s validation. The pandemic response eroded trust in public institutions, and RFK Jr.’s overhaul is tapping into a demand for transparency, choice, and real reform.

Public health bureaucrats who enforced some of the most sweeping mandates in modern American history are finally facing consequences. And as RFK Jr. continues to wage his ‘MAHA revolution,’ the message is clear: the Covid era is over — and so is the era of unaccountable science.