Three scientific papers cited by Robert F Kennedy Jr and anti-vaccine advocates to challenge vaccine safety are now under investigation, retracted, or removed from publication, marking a rare intervention by academic journals months or even years after critics first flagged serious methodological problems.
The papers had become central ammunition in the anti-vaccine movement. Kennedy, now US health secretary, relied on two of them for his 2023 book arguing unvaccinated children were healthier than vaccinated ones. A third study influenced the CDC to shift its position on vaccines and autism, contradicting scientific consensus. All three were cited by an anti-vaccine lawyer presenting to the federal vaccine advisory panel.
One 2021 paper by Neil Z Miller in Toxicology Reports claimed to find a link between vaccines and sudden infant death syndrome using reports from a vaccine safety database. A 2020 study in Sage Open Medicine, co-authored by Miller and Brian S Hooker, suggested vaccinated children had higher rates of developmental delays and asthma. A third from 2010 in the Journal of Toxicology and Environmental Health concluded boys vaccinated for hepatitis B faced higher autism risk.
Scientists who previously criticized the studies welcomed the journals' actions. With cases of whooping cough and measles rising across the United States, researchers argue these flawed papers have planted doubt in parents' minds about vaccine safety.
"These papers are poor science, it appears the authors are making the data fit their hypothesis that vaccines are harmful," said Dr Karina Top, a pediatrics professor at the University of Alberta, adding that anti-vaccine groups have skillfully misused scientific language to lend credibility to their claims.
The delay in action puzzled observers. Scientists began raising alarms about the studies immediately after publication, yet journals took years to respond. Top noted that in the six years since the Sage study appeared, it had been cited in other research and used to justify policy changes, "likely contributing to decreased vaccination rates and outbreaks of serious preventable infections."
Toxicology Reports removed Miller's VAERS study after identifying "serious methodological flaws." Elsevier, the publisher, stated the paper's "recommendations and conclusions may pose potential risks to public health." Magdalen Wind-Mozley, a forensic scientist who criticized the paper online months after its 2021 publication, had emailed a formal complaint to the journal in January 2022 but received no action for years.
The hepatitis B paper met a similar fate. In May, the Journal of Toxicology and Environmental Health retracted it after an independent statistical reviewer found fundamental flaws. The CDC had cited this very paper just months earlier when it changed its longstanding position on vaccines and autism, a shift made under Kennedy's direction. The reworked CDC page now states that "Studies supporting a link have been ignored by health authorities."
A viral TikTok and Instagram video by scientist Morgan McSweeney, viewed more than 5 million times, highlighted the absurdity of the CDC's reliance on the study. "This was a low-quality, very small study that was not replicated," McSweeney said in the clip, describing the research as essentially worthless.
The Sage Open Medicine paper investigating Miller and Hooker remains under investigation. The complaint, submitted anonymously by a pediatrician in January 2025, alleged data source problems and lack of disclosure. The journal attached an expression of concern in May and said it would make a decision once the authors responded to the raised concerns.
The authors have not ceded ground. Miller said the investigation involved false allegations and that an expression of concern was unwarranted. Melody Goodman, dean at NYU's School of Global Public Health and co-author of the hepatitis B paper, defended her methodology and noted the study was never meant as the final word on the issue. Hooker did not respond to requests for comment. Kennedy's HHS did not address whether the book would be updated.
Aaron Siri, who has served as Kennedy's lawyer, compared the journals' scrutiny to "targeted assassination" and stood by claims that no available evidence proves vaccines are "safe and effective," citing hundreds of other articles and trial documents.
McSweeney offered a sharper critique of how those in charge of vaccine policy now operate. "They have a strong opinion about what is true. And then they go looking for whatever scrap of low-quality evidence they can find to support that opinion," he said. "If that finding supports the story that they believe, they're willing to overlook data points from hundreds of thousands or millions of children."
Author James Rodriguez: "The timing here is maddening, but at least it's happening. What matters now is whether Kennedy's HHS acknowledges the retractions or doubles down on the discredited research."
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