Concerns Over Vaccine Safety Papers Lead to Retraction and Investigation

Recently, three scientific papers that questioned vaccine safety and were cited by the Trump administration to support contentious U.S. vaccine policy changes have either been removed, retracted, or are under investigation by their respective journals. This action has taken place over the last couple of months, although concerns around these studies were raised much earlier by scientists.

Robert F. Kennedy Jr., the U.S. health secretary known for promoting anti-vaccine views, used two of these scrutinized papers as backing for a 2023 co-authored book. In this book, he claimed that unvaccinated children enjoy better health compared to their vaccinated peers. Alarmingly, the Centers for Disease Control and Prevention (CDC) cited one of these papers when it altered its long-standing stance that vaccines don’t cause autism, thus contradicting the prevailing scientific consensus. All three studies were also referenced by an anti-vaccine attorney advocating for changes to childhood immunization schedules during a federal vaccine advisory panel meeting.

The delay in action from the journals remains unclear. Scientists who criticized these papers in the past viewed the recent actions as positive steps. They highlighted a troubling increase in vaccine-preventable diseases such as whooping cough and measles. These individuals argue that the studies in question have been pivotal in fostering doubt among parents, thereby undermining trust in vital vaccines.

Dr. Karina Top, a pediatrics professor at the University of Alberta, pointed out that misinformation about vaccines has been skillfully disseminated using flawed studies and misrepresented scientific terms. “These papers reflect poor scientific practices, as it seems the authors twisted the data to support the narrative that vaccines are harmful,” she stated.

Each of the three papers proposed that vaccinated children face higher health risks compared to their unvaccinated counterparts. However, they have been heavily criticized for methodological weaknesses and questionable analyses.

One paper by Neil Z. Miller, published in 2021 in *Toxicology Reports*, alleged a connection between vaccines and sudden infant death syndrome (SIDS). Another paper from 2020, co-authored by Miller and Brian S. Hooker in *Sage Open Medicine*, claimed vaccinated children showed higher rates of health issues like developmental delays and asthma. The third research, authored by Carolyn M. Gallagher and Melody S. Goodman in 2010, suggested that boys vaccinated for hepatitis B within the first four weeks of life were more likely to be diagnosed with autism.

Some of the researchers involved have expressed their disagreement with the journals’ decisions. The Department of Health and Human Services (HHS) did not respond to inquiries for comments.

Aaron Siri, a lawyer previously aligned with Kennedy, presented these three papers in a December session before a federal vaccine advisory committee. He described the scrutiny faced by the papers as a “targeted assassination” and maintained that he found no “available evidence” to validate that vaccines are “safe and effective,” despite claiming his analysis was based on hundreds of other studies and documents.

In the book *Vax-Unvax: Let the Science Speak*, co-authored with Hooker, Kennedy highlighted the aforementioned studies as crucial elements in substantiating the argument that vaccinated children suffer from higher health issues. The book interestingly notes the struggles faced to get the relevant paper published, mentioning that five medical journals rejected it before Sage Open Medicine finally accepted it, after a prolonged peer review process.

As of now, the HHS did not reply to questions regarding whether Kennedy plans to revise his book based on these developments.

Sage Open Medicine, which published the paper, attached an expression of concern on May 18, weeks after the Guardian raised inquiries about an anonymous complaint submitted to the journal in January 2025. This complaint, made by a pediatrician and scientist who wished to remain unnamed due to fears of harassment from anti-vaccine advocates, was prompted by witnessing the detrimental fears these studies instilled in parents regarding vaccination. They believed that such research has hampered childhood vaccination rates.

Neither Hooker nor Miller responded to requests for comments about their respective positions. Miller asserted that the investigation was due to false allegations concerning undisclosed data sources. He asserted that the expression of concern did not involve the validity of the paper’s findings.

“I’m not worried about this investigation because the allegations are untrue,” Miller remarked.

Sage’s spokesperson refrained from commenting on specifics while the investigation is underway. They mentioned that a final decision on the paper would be forthcoming after a thorough review of all relevant information.

Various scientists have expressed ongoing concerns about the paper since its publication. Top noted that over six years, this paper had been cited in other research and used to advocate for vaccine policy changes, likely contributing to lower vaccination rates and outbreaks of preventable diseases.

Top urged the journal and its editors to conduct a meticulous review of the peer-review process and their responses to past complaints, emphasizing the need for timelier actions in future contexts.

In November, the CDC referenced the hepatitis B paper when it reevaluated its position on the potential link between vaccines and autism at Kennedy’s behest, adjusting the top lines of their webpage to imply that studies supporting a link were being overlooked by health authorities.

HHS has yet to respond to inquiries about potential updates regarding this CDC webpage.

Scientist Morgan McSweeney, known for his online presence, created a video aimed at debunking the paper after observing the CDC’s changes, criticizing the study’s reliance on limited cases to assert that male newborns vaccinated with hepatitis B faced a higher autism diagnosis risk. He dismissed the study’s quality as low and noted its lack of replication, further emphasizing that the claims suggested by the authors are tenuous at best.

The paper was ultimately retracted on May 21 after an independent statistical reviewer identified significant methodological flaws, according to its retraction notice. The publisher, Taylor & Francis, stated that its inquiry initiated after concerns were communicated to them, preceding the CDC’s citation of the article.

Gallagher and Goodman, the authors of the retracted paper, expressed their disagreement with this decision. Goodman, the dean at New York University’s School of Global Public Health, defended the study’s methodology and reiterated that the research began as a student project, while acknowledging the limitations outlined in the paper.

“The aim was never to provide a definitive conclusion about this issue, which is precisely why we suggested further comprehensive studies, and which other researchers have pursued thereafter,” Goodman explained.

McSweeney suggested that while the issues stemmed from statistical limitations rather than malicious intentions, the paper’s usage by the CDC highlights a concerning trend regarding decision-making in vaccine policy. “They seem to cherry-pick data that supports their beliefs while ignoring broader evidence from larger populations,” he argued.

Miller’s 2021 paper drew on reports from the Vaccine Adverse Event Reporting System (VAERS) to suggest potential safety signals linking vaccination to SIDS. VAERS, a vaccine safety monitoring system, permits public reporting of any suspected adverse health events post-vaccination.

Following Miller’s publication, forensic scientist Magdalen Wind-Mozley criticized his paper online, pointing out numerous flaws like the misunderstanding of VAERS data. Although she formally complained to the journal in January 2022, she stated that she hadn’t seen any action taken until the recent developments.

While Elsevier, the publisher, claimed there were no formal complaints until 2025, it acknowledged that investigations prompted by concerns raised last year led to the identification of serious methodological flaws in linking vaccination to SIDS.

In a rare move, the journal decided to retract the paper, citing potential public health risks as a result of its recommendations, which could have had harmful implications in clinical practices.

Miller contested the publisher’s actions, asserting he had been asked to address what he deemed irrelevant or incorrect concerns. He criticized the journal for not explicitly detailing any methodological issues, defending his work robustly.

“I am firmly against the removal of my paper; this decision feels unjustified,” Miller stated.

Wind-Mozley commended the journal for retracting the paper but noted that the action was notably overdue, believing that it has adversely affected public opinions and behaviors regarding vaccines.

“Over the years since I first raised my concerns, this paper has likely caused substantial harm,” she concluded.