RFK Jr. Quietly Drives $50M Vaccine Safety Crusade Inside Federal Health Agencies

Health Secretary Robert F. Kennedy Jr. has gone nearly silent on vaccines in public — reportedly under White House pressure to avoid damaging Republican prospects in November's midterms — but behind closed doors he is running one of the most sweeping anti-vaccine research campaigns in federal history. Six people with direct knowledge of the effort, all speaking anonymously, described a sprawling inquiry spanning the FDA, CDC, NIH, and university partners, tasked with hunting for evidence linking vaccines to chronic disease, autism, and neurological disorders.

The initiative is being led by Martin Kulldorff, a Harvard-trained biostatistician who became a prominent critic of COVID vaccine mandates and now serves as the department's chief science and data officer. Kulldorff has genuine credentials — he helped detect an elevated risk of Guillain-Barré syndrome during the 2009 H1N1 vaccine rollout — but former colleagues express concern that his views shifted sharply during the pandemic. Court records show he earned $400 per hour as an expert witness for Kennedy in litigation against Merck over its Gardasil HPV vaccine in 2024, despite his own prior research finding the vaccine safe. Through the CDC alone, the project is estimated to cost $40 million to $50 million.

The research agenda reads like a greatest-hits list of Kennedy's long-held theories: comparing health outcomes in vaccinated versus unvaccinated children, revisiting the vaccine-autism link, and re-examining thimerosal — a mercury-based preservative largely phased out of U.S. vaccines but still present in some flu shots — despite decades of studies finding it harmless. A daylong planning meeting in late February brought together officials from HHS, CDC, and major health systems including Kaiser Permanente, which provides access to millions of patient records through the CDC's Vaccine Safety Datalink. Kennedy's senior counselor Dr. Sara Brenner, an FDA veteran who has publicly questioned vaccines, is expected to accelerate the studies.

The effort alarms mainstream vaccine scientists on multiple fronts. Epidemiologists warn that vaccinated-versus-unvaccinated comparisons are methodologically treacherous — vaccinated children see doctors more often and thus accumulate more diagnoses, which could be falsely attributed to vaccines. Critics also note that Kennedy has a documented pattern of dismissing inconvenient evidence: he called a landmark Danish study tracking 1.2 million children over 24 years a "deceitful propaganda stunt" because it didn't highlight a subgroup of roughly 50 children who showed slightly elevated Asperger's rates. Meanwhile, Kennedy has already reduced the recommended childhood vaccine schedule from 17 shots to 10, a move blocked in court. Public health veterans fear the new research will be selectively presented to drive further policy changes or legal action — Kennedy said in a 2024 podcast that building a scientific record of vaccine harms is how he plans to hold manufacturers liable in court.