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In September 2025, then-US Food and Drug Administration (FDA) Commissioner Dr Marty Makary publicly acknowledged that the agency was investigating reports of child deaths following Covid-19 vaccination.

“We do know at the FDA…that there had been children who have died from the COVID vaccine,” Makary said during a CNN interview.

By that stage, however, a fierce internal dispute had already emerged inside the FDA over what investigators believed the evidence showed – and whether the public should ever see the full findings.

“It really did feel like there was some sort of cover-up going on about the Covid-19 vaccines,” said one individual familiar with the discussions.

MD Reports spoke with several current/former agency officials, advisers, and individuals briefed on the discussions, all of whom requested anonymity because they were not authorised to publicly discuss internal FDA deliberations.

At the centre of the controversy was an internal FDA review led by Dr Tracy Beth Høeg, a physician-scientist who was working as a senior scientist inside the FDA’s vaccine division at the time.

FDA officials examined roughly 96 paediatric death reports submitted to the Vaccine Adverse Event Reporting System (VAERS), the government database used to detect potential vaccine-related adverse events.

The review included medical records, autopsy reports, pathology findings, and follow-up investigations conducted by agency staff.

About 25 deaths following Covid vaccination were ultimately considered serious enough for high-level internal discussion inside the agency.

The findings were expected to be presented at a September 2025 meeting of the CDC’s Advisory Committee on Immunisation Practices (ACIP), the federal panel that shapes US vaccine recommendations.

But before that could happen, details of the review leaked to the New York Times and the Washington Post.

Høeg quickly became the focus of intense media scrutiny and criticism from vaccine advocates and unnamed FDA officials who argued she was relying too heavily on VAERS reports and overstating preliminary findings.

People familiar with the fallout said some FDA staff strongly objected to Høeg’s methods and conclusions and allegedly sought to undermine her credibility by leaking details of the review.

The leak effectively ended plans for a public ACIP discussion and deepened divisions within the FDA over how the findings should be handled.

Some officials believed the findings warranted stronger warnings and greater transparency. Others feared public acknowledgement of vaccine-linked child deaths would damage confidence in the Covid vaccines.

“We know that there are these deaths that are due to the vaccine,” said one source, referring to myocarditis cases and published reports from countries including Korea and Israel.

The controversy intensified after then-FDA vaccine chief Dr Vinay Prasad ordered additional investigation into the deaths identified in Høeg’s review.

Months later, another leak brought the issue back into public view.

In November 2025, an internal memo circulated by Prasad became public. In it, Prasad acknowledged that “at least 10” children had died “after and because of receiving Covid-19 vaccination.”

He described the findings as “a profound revelation.”

“COVID-19 vaccines did result in the death of children,” Prasad wrote. “Dr. Hoeg was correct in her assessment.”

The memo triggered another round of backlash from media outlets and vaccine advocates, many of whom accused Prasad of overstating the evidence before the agency’s analysis had been finalised.

Inside Medicine reported on a Dec 5 memo about a subsequent FDA analysis using a World Health Organization causality framework, which classified zero deaths as “certain,” two as “probable/likely,” and five as “possible.”

But individuals involved in the discussions said pressure steadily mounted inside the agency to “downgrade” the findings with each successive review.

“It seemed like there was a lot of pressure to keep decreasing the number of deaths,” said one source.

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