Health Secretary Robert F. Kennedy Jr. has taken steps that could potentially impact public confidence in vaccines, according to public health experts. Despite political advisers urging him to prioritize more popular issues, Kennedy remains focused on vaccine policy, pursuing changes that some fear may undermine immunization efforts.

In recent months, the Department of Health and Human Services (HHS) has initiated multiple studies examining possible links between vaccines and a variety of health conditions. These studies, conducted both by established external researchers and political appointees, investigate associations between the childhood vaccination schedule and ailments including autoimmune diseases, asthma, seizures, and certain cancers. Some topics under review have previously been studied extensively and dismissed by mainstream scientists, raising concerns about the scientific rigor of the new inquiries.

Among the commissioned work is a $46 million contract awarded in August to the Vaccine Safety Datalink, a respected research network that has long analyzed vaccination data. Projects include examining potential correlations between vaccines and infections not targeted by immunization, such as ear infections and meningitis, as well as autoimmune disorders. While a 2025 Danish study on aluminum salts—commonly used in vaccines—found no link to asthma or other conditions, Kennedy criticized the findings as “deceptive.” His uneasy stance toward the Vaccine Safety Datalink’s work reflects longstanding skepticism; he recently described the research teams as biased.

Kennedy has also assigned political appointees to oversee studies, including David Geier, whose research claiming vaccine harm has been widely discredited. HHS has declined to comment on these internal studies but said their purpose is to “restore trust in vaccines” following the COVID-19 pandemic. Some public health advocates worry about a lack of transparency and potential misuse of research to fuel misinformation.

Further signaling a shift in vaccine oversight, Kennedy revived a federal task force on childhood vaccine safety, a group dissolved in 1998 but reinstated following a lawsuit by Kennedy’s own anti-vaccine organization, Children’s Health Defense. President Donald Trump directed the task force—comprising leaders from the CDC, NIH, and FDA—to deliver a report to the White House next month. The task force has sought public input on new ways to recommend vaccines, including “conditional recommendations” and “shared clinical decision making,” which could lower vaccination rates. Over 35,000 comments have been submitted, with only a fraction publicly available. Critics, including Democratic state attorneys general led by California’s Rob Bonta, have warned that proposed changes are “unwarranted and dangerous,” likely to erode public trust.

Kennedy has also targeted the Vaccine Injury Compensation Program, a specialized court set up in 1986 to compensate individuals who claim vaccine-related injuries, while protecting manufacturers from most lawsuits. He has criticized the program as inefficient and corrupt, although acknowledging it has paid roughly $5.6 billion to about 13,500 claimants over its history. In 2025, Kennedy brought in vaccine injury attorney Andrew Downing to review the system. Since then, Aaron Siri, another vaccine litigator aligned with Kennedy, petitioned HHS to add more injuries to the court’s vaccine injury table, which would expedite compensation for those claims.

Siri’s petition, submitted on behalf of the Informed Consent Action Network—an organization linked to Kennedy’s 2024 presidential campaign—calls for including more than 150 conditions flagged in 2009 as “associated” with vaccines. Public health experts caution that many of these conditions appear on vaccine package inserts without established causality. They argue that broadening the table without scientific support would increase vaccine hesitancy, complicate compensation for legitimate injuries, and strain the system.

These developments underscore ongoing tensions within federal vaccine policy, with advocates warning that some of Kennedy’s initiatives risk undermining decades of public health progress by fostering skepticism and confusion about vaccine safety.