Three studies that have long been used to question vaccine safety and were invoked to justify changes to US vaccine policy have now been retracted, removed, or placed under investigation – years after scientists first raised alarms about their credibility.
The actions, taken by the journals that published the papers over the past two months, come after the studies were cited by the US Centers for Disease Control and Prevention (CDC) in a policy shift, relied upon by Health Secretary Robert F Kennedy Jr in his 2023 book, and presented by an anti-vaccine lawyer to a federal advisory panel. Public health experts say the research has been weaponised to erode confidence in childhood immunisations, contributing to rising outbreaks of preventable diseases.
Retractions and Investigations
One of the papers, published in 2021 by Neil Z Miller in the journal Toxicology Reports, claimed to find a link between vaccination and sudden infant death syndrome (Sids). The journal’s publisher, Elsevier, issued an apology and removed the paper after an investigation identified “serious methodological flaws” in the use of data from the Vaccine Adverse Event Reporting System (VAERS). VAERS is a passive monitoring system where anyone can report a suspected adverse event; the CDC and the Food and Drug Administration have long stressed that it cannot be used to infer cause and effect, that it often lacks detail and is subject to errors and under-reporting. Elsevier said the paper’s conclusions “may pose potential risks to public health” and could lead to patient harm. Miller, who is not a scientist but a “medical research journalist” and director of the Thinktwice Global Vaccine Institute, said he “strongly opposed” the removal and that the allegations against his work were false.
A second study, published in 2020 by Sage Open Medicine and co-authored by Miller and Brian S Hooker, suggested that vaccinated children had higher rates of developmental delays and asthma than unvaccinated children. The journal attached an expression of concern on 18 May and said the paper was under investigation. The action followed a complaint submitted anonymously by a paediatrician and scientist who said they had seen how such studies frighten parents. Hooker, a biochemical engineer whose son has autism and who has previously had work retracted over methodological concerns, did not respond to requests for comment. Miller said the investigation concerned “false allegations” about the data source and not the methodology. Sage said it would not comment during the investigation.
The third paper, published in 2010 by Carolyn M Gallagher and Melody S Goodman in the Journal of Toxicology and Environmental Health, Part A, found that boys vaccinated for hepatitis B in their first four weeks of life were more likely to be diagnosed with autism. The journal retracted it on 21 May after an independent statistical reviewer concluded there were “fundamental methodological flaws”. The study, which used data from the National Health Interview Survey from 1997 to 2002, had a critically small number of autism cases and inadequate statistical analysis. The authors disagreed with the retraction; Goodman, a biostatistician and dean at New York University’s School of Global Public Health, said the paper was never meant to be the final word and that they had called for larger studies.
How Flawed Studies Undermine Vaccine Confidence
All three papers share a common narrative: that vaccinated children face greater health risks than the unvaccinated. But scientists say their methodologies are so weak that they should never have shaped policy or public debate. Dr Karina Top, a professor of paediatrics at the University of Alberta, said the studies appear to have been designed to fit a predetermined conclusion. “People and organisations intent on spreading vaccine misinformation have been very savvy in their misuse of scientific terms, such as ‘gold-standard science’, and publishing flawed studies to give their claims the appearance of credibility and confuse the public,” she said. “These papers are poor science, it appears the authors are making the data fit their hypothesis that vaccines are harmful.”
The impact has been profound. The CDC cited the 2010 hepatitis B paper in November when, at Kennedy’s direction, it changed its long-standing position that vaccines do not cause autism. The reworked CDC webpage now states that “Studies supporting a link have been ignored by health authorities”. The National Medical Association, a group representing Black physicians, has said there is “no credible scientific evidence demonstrating that vaccines cause autism”. Demetre Daskalakis, former director of the CDC’s National Center for Immunization and Respiratory Diseases, described the changes as “a national embarrassment”.
Kennedy co-wrote his 2023 book Vax-Unvax: Let the Science Speak with Hooker, and the Miller–Hooker paper served as a crucial pillar in a chapter arguing that vaccinated children suffer higher rates of asthma, developmental delays and gastrointestinal disorders. The book itself, described as being “based on over one hundred studies in the peer-reviewed literature”, reveals that five medical journals rejected that paper before Sage Open Medicine accepted it, and that the journal struggled to find peer reviewers, with the process taking 11 months. Kennedy and Hooker previously worked together at the anti-vaccine group Children’s Health Defense, where Hooker now serves as chief scientific officer.
Aaron Siri, a lawyer who has represented Kennedy, cited all three papers in a presentation to the federal vaccine advisory panel in December. He has described the recent scrutiny of the studies as a “targeted assassination” and maintains that there is no “available evidence” that vaccines are safe and effective, saying his assessment rests on hundreds of other articles and trial documents.
Morgan McSweeney, a scientist who posts online as Dr.Noc, made a video debunking the hepatitis B paper after the CDC cited it. He noted that the study relied on a very small number of cases and had not been replicated. “This was a low-quality, very small study that was not replicated,” he said. “And maybe that’s a little bit true, because the studies they’re showing here are worth less than a fart in the summer breeze.” The video has since amassed more than five million views. McSweeney said the way the CDC used the paper showed that those in charge of US vaccine policy “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. If that finding supports the story that they believe, they’re willing to overlook data points from hundreds of thousands or millions of children and go with the one that fits their story.”
Delayed Action and Lasting Harm
Scientists raised concerns about the Miller–Hooker paper within days of its publication in 2020, yet the journal only attached an expression of concern five years later, after a formal complaint. The paediatrician who submitted that complaint told this newsroom they made the complaint in January 2025 because they had seen how such studies scare parents away from vaccinating their children. Dr Top called on the publisher to conduct a thorough review of its peer-review process and to improve the timeliness of its response. The 2010 hepatitis B paper had also been criticised for years; an independent statistical review only began after concerns were raised with the publisher – before the CDC cited it, according to Taylor & Francis, the parent company. Yet the CDC had already updated its website.
The Miller Sids paper was flagged by Magdalen Wind-Mozley, a forensic scientist and vaccine advocate who works with the Oxford Vaccine Group, within months of its publication in 2021. She emailed a complaint to Toxicology Reports in January 2022 and followed up, but was not aware of any action at the time. Elsevier said its records do not show a formal complaint until 2025. After concerns were raised last year, the journal launched an investigation and ultimately removed the paper. Wind-Mozley praised the removal but said it was far too late. “In the intervening years since her initial complaints, she said, ‘It will have done so much harm.’”
That harm is measurable. Public health officials across the US and in the UK are reporting a rise in vaccine-preventable diseases. In England, whooping cough cases in 2024 were more than 1,600% higher than in 2023, and measles cases reached their highest number in over two decades, causing the UK to lose its measles elimination status. Outbreaks are disproportionately affecting areas with lower vaccination rates. While a 2025 UK Health Security Agency survey found that 85% of parents still believe childhood vaccines are safe, confidence has declined since 2015, and the spread of flawed studies through social media – which only 3% of parents rank as a trusted source – continues to fuel doubt.
The Department of Health and Human Services (HHS) did not respond to questions about whether Kennedy would update his book or whether the CDC would revise its vaccine safety webpage. Kennedy has begun a “comprehensive review of the causes of autism”, according to HHS. Meanwhile, the three studies that helped shape the current policy landscape have been stripped of their scientific standing – but only after years of use by those determined to undermine the safety of vaccines.
